Variant report

Variant	rs3127599
Chromosome Location	chr6:160907134-160907135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10945675	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1112073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255830	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2457567	0.90[ASN][1000 genomes]
rs2504922	1.00[CHB][hapmap]
rs3123629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3123631	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3124784	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3124785	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3124786	0.84[ASN][1000 genomes]
rs3127568	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3127569	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3127595	0.87[ASN][1000 genomes]
rs3127596	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3127602	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129086	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs58432601	0.86[ASN][1000 genomes]
rs62441868	0.86[ASN][1000 genomes]
rs62441870	0.88[ASN][1000 genomes]
rs62441872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916433	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs7742018	0.87[ASN][1000 genomes]
rs7744658	1.00[CHB][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs7761293	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs9347407	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs9347408	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9355805	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]
rs9365166	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[ASN][1000 genomes]
rs9456538	0.83[GIH][hapmap]
rs9456545	0.87[ASN][1000 genomes]
rs9456546	0.87[ASN][1000 genomes]
rs9457930	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	esv6519	chr6:160877633-160956593	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv886813	chr6:160877640-160940120	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv3378121	chr6:160877757-160956624	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3475083	chr6:160877837-160956581	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv3475084	chr6:160877837-160956581	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv3351253	chr6:160896879-160975729	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv970183	chr6:160903531-160908726	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
17	nsv525990	chr6:160903622-160970963	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary heart disease	19198611	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160884400-160928200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:160893800-160921800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:160893800-160923200	Strong transcription	Liver	Liver
4	chr6:160894400-160915200	Weak transcription	Esophagus	oesophagus
5	chr6:160894800-160923800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:160897000-160914200	Weak transcription	Gastric	stomach
7	chr6:160897800-160908400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:160897800-160923000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:160898000-160908000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:160898000-160922800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:160900200-160911400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:160900400-160923400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:160901400-160909600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:160901600-160908800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:160902000-160921000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:160902200-160908200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr6:160902200-160914200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:160902400-160908000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:160902600-160908200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:160902800-160915400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:160902800-160923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:160903000-160908400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:160903000-160913200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:160903200-160908200	Strong transcription	Aorta	Aorta
25	chr6:160903200-160909200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:160903200-160914000	Weak transcription	Brain Angular Gyrus	brain
27	chr6:160903400-160913800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:160903400-160923400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:160903600-160912400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:160903600-160923800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:160903600-160924000	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:160904400-160920600	Weak transcription	Pancreas	Pancrea
33	chr6:160904600-160912000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:160904800-160924000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:160905000-160911400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:160905200-160911200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:160905200-160923000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:160905400-160923400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:160905400-160924800	Weak transcription	Ovary	ovary

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