Variant report

Variant	rs2288990
Chromosome Location	chr1:153318008-153318009
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153314988..153319996-chr1:153321870..153325921,5	K562	blood:
2	chr1:153315494..153319256-chr1:153320325..153322468,4	MCF-7	breast:
3	chr1:153312042..153314259-chr1:153317727..153320410,2	MCF-7	breast:
4	chr1:153310086..153312333-chr1:153317510..153319218,3	K562	blood:
5	chr1:153316827..153319773-chr1:153324804..153327111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10888551	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11589286	0.96[ASN][1000 genomes]
rs12139503	0.89[ASN][1000 genomes]
rs1897695	0.93[ASN][1000 genomes]
rs2117130	0.93[ASN][1000 genomes]
rs2916220	0.93[ASN][1000 genomes]
rs2916223	0.96[ASN][1000 genomes]
rs2916224	0.93[ASN][1000 genomes]
rs2916225	0.93[ASN][1000 genomes]
rs2916226	0.93[ASN][1000 genomes]
rs2916227	0.93[ASN][1000 genomes]
rs2916228	0.93[ASN][1000 genomes]
rs2916229	0.93[ASN][1000 genomes]
rs2916230	0.93[ASN][1000 genomes]
rs2916231	0.96[ASN][1000 genomes]
rs2916232	0.93[ASN][1000 genomes]
rs2916233	0.90[ASN][1000 genomes]
rs2916235	0.93[ASN][1000 genomes]
rs2916236	0.93[ASN][1000 genomes]
rs2987759	0.93[ASN][1000 genomes]
rs2987760	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs2987763	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2987764	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2987766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs2987767	0.93[ASN][1000 genomes]
rs2987768	0.93[ASN][1000 genomes]
rs2987769	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs3006411	0.93[ASN][1000 genomes]
rs3006427	0.92[ASN][1000 genomes]
rs3006431	0.96[ASN][1000 genomes]
rs3006434	0.96[ASN][1000 genomes]
rs3006439	0.96[ASN][1000 genomes]
rs3006440	0.93[ASN][1000 genomes]
rs3006441	0.93[ASN][1000 genomes]
rs3006444	0.98[ASN][1000 genomes]
rs3006445	0.91[ASN][1000 genomes]
rs3006446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs3006447	0.91[ASN][1000 genomes]
rs3006472	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs3006473	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs3014853	0.93[ASN][1000 genomes]
rs3014854	0.91[ASN][1000 genomes]
rs3014855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs3014858	0.98[ASN][1000 genomes]
rs3125234	0.91[ASN][1000 genomes]
rs3753460	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806230	0.96[ASN][1000 genomes]
rs9435978	0.96[ASN][1000 genomes]
rs9435979	0.92[ASN][1000 genomes]
rs9435983	0.96[ASN][1000 genomes]
rs9436076	0.96[ASN][1000 genomes]
rs9436077	0.96[ASN][1000 genomes]
rs9436084	0.93[ASN][1000 genomes]
rs957195	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9661293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9970937	0.90[ASN][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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 miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv999024	chr1:153255005-153325685	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3421067	chr1:153285224-153321348	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv6733	chr1:153285308-153321521	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153314200-153319400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:153314800-153318200	Enhancers	Fetal Intestine Large	intestine
3	chr1:153315200-153318800	Enhancers	Fetal Intestine Small	intestine
4	chr1:153315200-153319200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:153315200-153319600	Enhancers	Fetal Thymus	thymus
6	chr1:153315600-153319000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:153315600-153319200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:153315600-153319200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:153315800-153318400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:153315800-153319200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:153316000-153318800	Enhancers	Lung	lung
12	chr1:153316000-153319200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:153316000-153319200	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:153316200-153319400	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:153316200-153330400	Weak transcription	Right Atrium	heart
16	chr1:153316600-153318200	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:153316600-153318800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:153316600-153319200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr1:153316600-153319200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:153316800-153318200	Enhancers	Pancreas	Pancrea
21	chr1:153316800-153319200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:153316800-153319200	Enhancers	Thymus	Thymus
23	chr1:153316800-153320800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:153317000-153318200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr1:153317000-153318800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:153317000-153318800	Enhancers	Spleen	Spleen
27	chr1:153317000-153319200	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr1:153317000-153323200	Weak transcription	HMEC	breast
29	chr1:153317200-153318200	Enhancers	K562	blood
30	chr1:153317200-153319200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:153317200-153319400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:153317200-153321600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:153317400-153319400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:153317600-153318600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:153317600-153319400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr1:153317600-153320400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:153317800-153318200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr1:153317800-153318200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:153317800-153318400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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