Variant report

Variant	rs381472
Chromosome Location	chr6:5111196-5111197
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs200844	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs200860	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200866	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs200869	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs364857	0.85[ASN][1000 genomes]
rs373696	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs374117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs378359	0.82[CEU][hapmap]
rs379508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385481	0.82[CEU][hapmap]
rs388597	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392847	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs393055	0.85[ASN][1000 genomes]
rs393300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs393628	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs394252	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs411483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411893	0.83[ASN][1000 genomes]
rs414986	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs417629	0.95[ASN][1000 genomes]
rs424006	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs434706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438934	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs439911	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs441463	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs441482	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs445229	0.83[ASN][1000 genomes]
rs445342	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs452908	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs453331	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs456209	1.00[JPT][hapmap]
rs458108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458283	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458743	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461117	0.81[EUR][1000 genomes]
rs461465	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs462327	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs465453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465481	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs466285	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs591481	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs592775	0.81[EUR][1000 genomes]
rs606033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs620360	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661578	0.85[ASN][1000 genomes]
rs667543	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9405257	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	esv3408271	chr6:5111027-5111246	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5096000-5112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:5097600-5112800	Weak transcription	K562	blood
4	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
5	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:5102800-5111600	Weak transcription	Thymus	Thymus
8	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:5103200-5114000	Weak transcription	Dnd41	blood
11	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:5103800-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:5103800-5112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:5104200-5112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:5104200-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:5105000-5113200	Strong transcription	HepG2	liver
17	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:5105800-5125600	Weak transcription	Ovary	ovary
20	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:5106800-5111800	Strong transcription	Fetal Stomach	stomach
22	chr6:5107200-5112600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:5107600-5111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:5107800-5111600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:5107800-5112200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
27	chr6:5108000-5113600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:5108200-5112200	Weak transcription	Aorta	Aorta
29	chr6:5108200-5112800	Strong transcription	Spleen	Spleen
30	chr6:5108400-5112400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:5108600-5111800	Weak transcription	Fetal Thymus	thymus
32	chr6:5108600-5112200	Weak transcription	Fetal Lung	lung
33	chr6:5109000-5111800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:5109000-5112200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:5109000-5113800	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:5109000-5116400	Weak transcription	Brain Germinal Matrix	brain
37	chr6:5109200-5111800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:5109200-5111800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:5109200-5112000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:5109200-5118600	Weak transcription	Esophagus	oesophagus
41	chr6:5109200-5121800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:5109200-5130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:5109400-5111800	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:5109400-5112200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:5109400-5121600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:5109600-5112000	Weak transcription	HMEC	breast
47	chr6:5109600-5112200	Weak transcription	Placenta	Placenta
48	chr6:5109800-5111600	Weak transcription	Right Atrium	heart
49	chr6:5109800-5111800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:5109800-5112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links