Variant report

Variant	rs2762879
Chromosome Location	chr1:144890258-144890259
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:144889740..144892703-chr1:146500075..146502138,3	MCF-7	breast:
2	chr1:144888141..144890870-chr1:145070504..145072082,2	K562	blood:
3	chr1:144881667..144883836-chr1:144885018..144890367,4	K562	blood:

Variant related genes	Relation type
ENSG00000178104	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10910730	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1539655	1.00[YRI][hapmap]
rs1539656	1.00[CHB][hapmap]
rs1616118	1.00[CHB][hapmap]
rs1621108	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1625512	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1627675	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1630994	0.88[CHB][hapmap]
rs1663855	0.86[CHB][hapmap]
rs1663862	1.00[CHB][hapmap]
rs1663873	1.00[CHB][hapmap]
rs1664028	1.00[CHB][hapmap]
rs1747959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1778121	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1778142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1778601	0.86[CHB][hapmap]
rs1778603	1.00[YRI][hapmap]
rs1778613	1.00[YRI][hapmap]
rs1778660	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs1778746	0.88[CHB][hapmap]
rs1778748	0.86[CHB][hapmap]
rs1778759	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1778761	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs1778763	0.88[CHB][hapmap]
rs1778772	1.00[CHB][hapmap]
rs2489083	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs2590078	0.82[CHB][hapmap]
rs2590125	0.82[YRI][hapmap]
rs2653711	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2762723	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2762736	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2762863	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2798894	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2798895	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2798904	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs719603	1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014985	chr1:144007818-144949963	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
2	esv1828275	chr1:144274482-145098718	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
3	nsv1001693	chr1:144471974-145290292	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	311 gene(s)	inside rSNPs	diseases
4	nsv872210	chr1:144617179-144924792	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3359519	chr1:144674517-144950252	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3493993	chr1:144674667-144950191	Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3493994	chr1:144674667-144950191	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1830469	chr1:144679113-145320996	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv436611	chr1:144709882-144978624	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv435736	chr1:144709964-144987027	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv946244	chr1:144811539-144897508	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv831315	chr1:144813808-144962476	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv872211	chr1:144828599-144894697	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	esv2761854	chr1:144832255-144921857	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	esv2630464	chr1:144841079-144893666	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
16	nsv872212	chr1:144850451-145073750	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
17	nsv872213	chr1:144865454-145033984	Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
18	nsv1009283	chr1:144865627-144950969	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv1005230	chr1:144865627-145151820	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
20	esv1828244	chr1:144865627-145243316	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
21	nsv469838	chr1:144869935-145009137	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
22	nsv482650	chr1:144869935-145009137	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
23	nsv471603	chr1:144869936-145009137	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
24	esv2753760	chr1:144873327-145041016	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
25	esv2753260	chr1:144873327-145129144	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
26	nsv2	chr1:144874979-144913548	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
27	nsv2633	chr1:144874979-144913548	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
28	nsv872214	chr1:144875799-145195645	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
29	nsv1009955	chr1:144880316-144935874	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
30	esv1010993	chr1:144881391-144919679	ZNF genes & repeats Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
31	nsv1000251	chr1:144884237-144949963	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
32	nsv821620	chr1:144885908-145095806	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
33	nsv1011358	chr1:144887881-144901738	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
34	nsv999753	chr1:144887881-144991278	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
35	nsv1014504	chr1:144889465-144970212	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
36	esv2753261	chr1:144889465-145041016	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:144850000-144894000	Strong transcription	Stomach Smooth Muscle	stomach
2	chr1:144850400-144894200	Strong transcription	Brain Germinal Matrix	brain
3	chr1:144852200-144913200	Weak transcription	Stomach Mucosa	stomach
4	chr1:144868600-144892400	Weak transcription	Fetal Thymus	thymus
5	chr1:144869400-144905000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:144874600-144901600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:144874800-144906600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:144875000-144891400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:144875000-144893600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:144875000-144911000	Weak transcription	Thymus	Thymus
11	chr1:144876800-144892400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:144877400-144902200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:144881000-144891800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:144881200-144890800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:144881400-144890600	Weak transcription	Fetal Lung	lung
16	chr1:144881400-144891000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:144881400-144904800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:144882000-144892600	Weak transcription	HepG2	liver
19	chr1:144882600-144891800	Weak transcription	Pancreas	Pancrea
20	chr1:144883000-144890400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:144883000-144891800	Weak transcription	Spleen	Spleen
22	chr1:144883000-144892400	Weak transcription	Esophagus	oesophagus
23	chr1:144883000-144893200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:144883000-144902600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:144883000-144902800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:144883000-144911600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:144883200-144890800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:144883200-144891000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:144883200-144891800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:144883200-144902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:144883600-144890400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:144883600-144892200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:144883600-144893200	Weak transcription	Fetal Kidney	kidney
34	chr1:144884200-144892200	Weak transcription	Ovary	ovary
35	chr1:144885400-144890400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:144885800-144890400	Weak transcription	Fetal Brain Male	brain
37	chr1:144885800-144891400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr1:144886400-144890400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:144886400-144891200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:144886600-144892400	Weak transcription	Colonic Mucosa	Colon
41	chr1:144886800-144891000	Weak transcription	Fetal Intestine Large	intestine
42	chr1:144887200-144904400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:144887400-144891800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:144887800-144892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:144887800-144894200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:144887800-144894200	Strong transcription	Brain Angular Gyrus	brain
47	chr1:144887800-144902600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:144888000-144890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:144888000-144890600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:144888000-144890800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links