Variant report

Variant	rs3920615
Chromosome Location	chr10:6176780-6176781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10400124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400125	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10905880	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10905881	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11256945	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12218872	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12219621	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12219630	0.92[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571538	0.94[JPT][hapmap]
rs4747887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4747888	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4750012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4750015	0.82[ASN][1000 genomes]
rs4750016	0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7099083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6168200-6178200	Weak transcription	A549	lung
2	chr10:6171200-6177000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:6171200-6178600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:6171400-6183200	Weak transcription	Right Atrium	heart
5	chr10:6172200-6178400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr10:6172200-6178400	Weak transcription	Adipose Nuclei	Adipose
7	chr10:6172200-6182800	Weak transcription	Brain Angular Gyrus	brain
8	chr10:6172400-6178200	Weak transcription	Esophagus	oesophagus
9	chr10:6172400-6181600	Weak transcription	Spleen	Spleen
10	chr10:6172400-6182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:6172600-6176800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:6173000-6176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:6173000-6181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:6173200-6178400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:6173400-6176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr10:6173400-6176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:6173400-6178000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:6173400-6178000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:6173600-6177800	Weak transcription	NHDF-Ad	bronchial
20	chr10:6173600-6178000	Weak transcription	NH-A	brain
21	chr10:6173600-6178000	Weak transcription	NHLF	lung
22	chr10:6174400-6177000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:6175000-6176800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr10:6175200-6176800	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr10:6175600-6176800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:6175600-6176800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr10:6175600-6176800	Enhancers	GM12878-XiMat	blood
28	chr10:6176200-6177200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr10:6176200-6177200	Enhancers	Fetal Thymus	thymus
30	chr10:6176200-6177400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr10:6176200-6179200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:6176200-6179200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr10:6176400-6177200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:6176400-6177200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:6176400-6179400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:6176600-6176800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr10:6176600-6176800	Enhancers	Small Intestine	intestine
38	chr10:6176600-6177200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:6176600-6177200	Enhancers	Thymus	Thymus
40	chr10:6176600-6178200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr10:6176600-6178400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:6176600-6179000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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