Variant report

Variant	rs677878
Chromosome Location	chr15:42495264-42495265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42490478..42492456-chr15:42492848..42495369,2	K562	blood:
2	chr15:42493109..42497444-chr15:42498289..42501536,5	K562	blood:
3	chr15:42446822..42448866-chr15:42493306..42496254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168907	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000261002	Chromatin interaction
ENSG00000207712	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10775126	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10851407	0.89[EUR][1000 genomes]
rs10851408	0.89[EUR][1000 genomes]
rs10851409	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11070370	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs11631917	0.89[EUR][1000 genomes]
rs11631983	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs12438369	0.88[CEU][hapmap]
rs12438453	0.89[CEU][hapmap]
rs12438562	0.82[EUR][1000 genomes]
rs12441642	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12441700	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs12594162	0.89[EUR][1000 genomes]
rs12917101	0.89[EUR][1000 genomes]
rs1359003	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1359004	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1619030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624183	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs1626437	0.81[JPT][hapmap]
rs1659212	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1659213	0.81[CHB][hapmap]
rs1659217	0.82[EUR][1000 genomes]
rs1659218	0.81[CHB][hapmap]
rs1678985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678989	0.81[JPT][hapmap]
rs1678991	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678992	0.81[CHB][hapmap]
rs1678993	0.81[CHB][hapmap]
rs1679002	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679012	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1703750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703754	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1703755	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1712418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712421	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2138831	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2289295	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs2407707	1.00[CEU][hapmap]
rs2412682	0.89[EUR][1000 genomes]
rs2412685	0.89[EUR][1000 genomes]
rs2412705	0.82[EUR][1000 genomes]
rs2918459	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs2918460	0.81[CHB][hapmap]
rs2918461	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs3743006	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs4329897	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs4923940	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs4923943	0.84[EUR][1000 genomes]
rs4924645	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4924648	0.89[EUR][1000 genomes]
rs4924653	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs4924658	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs4924660	0.84[EUR][1000 genomes]
rs4924674	1.00[CEU][hapmap]
rs58313689	0.88[EUR][1000 genomes]
rs59132828	0.82[EUR][1000 genomes]
rs598360	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622714	0.81[ASN][1000 genomes]
rs624841	0.81[ASN][1000 genomes]
rs633934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493027	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs660126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678778	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs681029	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7166785	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs7168709	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs7175863	0.82[EUR][1000 genomes]
rs7177120	0.81[EUR][1000 genomes]
rs7179709	0.81[CHB][hapmap]
rs7181742	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs7183015	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs7183546	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs751572	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs765830	0.82[EUR][1000 genomes]
rs8024113	0.90[CHB][hapmap]
rs8024732	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs8025601	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8031315	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs8033080	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8036046	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036380	0.82[EUR][1000 genomes]
rs8036596	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs8037020	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs9672382	0.94[EUR][1000 genomes]
rs9920921	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42460000-42499200	Weak transcription	A549	lung
2	chr15:42460000-42499800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42466000-42498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42475000-42499200	Weak transcription	Stomach Mucosa	stomach
5	chr15:42476800-42499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42477200-42497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:42478400-42498600	Weak transcription	Gastric	stomach
8	chr15:42480200-42496000	Weak transcription	Esophagus	oesophagus
9	chr15:42480400-42498600	Weak transcription	Small Intestine	intestine
10	chr15:42480400-42498800	Weak transcription	Right Ventricle	heart
11	chr15:42480600-42496000	Weak transcription	Spleen	Spleen
12	chr15:42481200-42499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:42481600-42497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:42481600-42497600	Weak transcription	HUVEC	blood vessel
15	chr15:42481600-42498600	Weak transcription	Fetal Brain Male	brain
16	chr15:42482800-42499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:42483200-42499400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:42483400-42498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:42483400-42498600	Weak transcription	Fetal Kidney	kidney
20	chr15:42483600-42497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:42483600-42498600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:42483600-42498600	Weak transcription	K562	blood
23	chr15:42483600-42499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:42483800-42499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:42484000-42499200	Weak transcription	HMEC	breast
26	chr15:42484400-42495800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:42484400-42499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:42484800-42498600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:42484800-42498800	Weak transcription	NHEK	skin
30	chr15:42484800-42499400	Weak transcription	Left Ventricle	heart
31	chr15:42487000-42496000	Weak transcription	Pancreas	Pancrea
32	chr15:42487400-42498400	Weak transcription	HepG2	liver
33	chr15:42489600-42496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:42489600-42496600	Strong transcription	Primary B cells from cord blood	blood
35	chr15:42490000-42499400	Weak transcription	Aorta	Aorta
36	chr15:42490000-42499400	Weak transcription	Colonic Mucosa	Colon
37	chr15:42490400-42495800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:42490400-42498600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:42490400-42498600	Weak transcription	NHDF-Ad	bronchial
40	chr15:42490800-42498600	Weak transcription	Fetal Intestine Small	intestine
41	chr15:42490800-42499200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:42491000-42497600	Weak transcription	Dnd41	blood
43	chr15:42491000-42499000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:42491000-42499200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:42491000-42499200	Weak transcription	NHLF	lung
46	chr15:42491000-42499400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:42491200-42498600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:42491400-42495600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:42491400-42499200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:42491400-42499200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links