Variant report

Variant	rs9948
Chromosome Location	chr2:97500800-97500801
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97499234..97501517-chr2:97522388..97524057,2	MCF-7	breast:
2	chr2:97500023..97502292-chr2:97598667..97600575,2	MCF-7	breast:
3	chr2:97498894..97501662-chr2:97504952..97507500,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11897786	0.87[CEU][hapmap]
rs1317911	0.87[CEU][hapmap]
rs1320146	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1320149	0.87[CEU][hapmap]
rs13419073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs17119562	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17119564	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17119591	1.00[CHB][hapmap]
rs17119598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2139406	1.00[GIH][hapmap]
rs2276654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2280356	1.00[GIH][hapmap]
rs2872633	1.00[GIH][hapmap]
rs3731940	1.00[GIH][hapmap]
rs3731941	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs6576986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6576987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap]
rs6576989	0.88[MEX][hapmap];0.89[TSI][hapmap]
rs6751132	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6753987	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs6756482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6758151	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7580942	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs7594727	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs7608621	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs9973492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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 miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS 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 target site	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Erectile dysfunction and prostate cancer treatment	20932654	GWAS catalog

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
2	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
3	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
4	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
5	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:97487400-97501800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:97487400-97504200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:97487600-97504600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:97488000-97501200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:97488200-97501200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:97488200-97501800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:97488400-97501200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:97488600-97501200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:97488600-97504600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:97488800-97501600	Strong transcription	Brain Angular Gyrus	brain
16	chr2:97489200-97501400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:97489400-97501200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:97489400-97506600	Strong transcription	Dnd41	blood
19	chr2:97489400-97509000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr2:97489800-97501200	Strong transcription	Fetal Brain Female	brain
21	chr2:97490200-97507800	Strong transcription	Brain Anterior Caudate	brain
22	chr2:97490400-97501800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:97490600-97501200	Strong transcription	HepG2	liver
24	chr2:97490600-97501600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:97490600-97504000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:97491800-97501000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:97492400-97501200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr2:97496200-97512400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:97496600-97504200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:97496600-97504200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:97497800-97501200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:97497800-97501600	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr2:97498000-97501200	Strong transcription	Primary B cells from cord blood	blood
34	chr2:97498200-97501200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:97498400-97501200	Strong transcription	GM12878-XiMat	blood
36	chr2:97498400-97513400	Weak transcription	NHEK	skin
37	chr2:97499000-97501000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:97499000-97502600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:97499000-97504800	Weak transcription	HMEC	breast
40	chr2:97499000-97505200	Weak transcription	NH-A	brain
41	chr2:97499200-97501000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:97499200-97501600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:97499200-97501800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:97499200-97503200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr2:97499200-97503400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:97499200-97503400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:97499200-97503400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:97499200-97503400	Weak transcription	Spleen	Spleen
49	chr2:97499200-97503800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:97499200-97503800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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