Variant report

Variant	rs4257888
Chromosome Location	chr6:121588290-121588291
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10499105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10782210	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11964400	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11968501	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12524471	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12525057	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12525337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12526158	0.89[EUR][1000 genomes]
rs12526903	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12527407	0.82[ASN][1000 genomes]
rs12527618	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12527748	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12529567	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12529694	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530424	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273766	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273772	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273774	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273775	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273776	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1314812	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1621008	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1697446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17083387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17083393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17083441	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1948733	0.81[AFR][1000 genomes]
rs2133993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2173837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2173838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2884396	1.00[CEU][hapmap]
rs34349558	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4458731	0.82[AFR][1000 genomes]
rs4466276	0.84[AFR][1000 genomes]
rs4483022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4527742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4543411	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4585603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4945681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4945682	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4946540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4946546	0.82[ASN][1000 genomes]
rs4946548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4946551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55642029	0.82[AFR][1000 genomes]
rs59480217	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6569179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6569182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6569183	0.85[AFR][1000 genomes]
rs6569184	0.86[AFR][1000 genomes]
rs6569194	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6912500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916773	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6918831	0.80[AMR][1000 genomes]
rs6920459	0.84[AFR][1000 genomes]
rs6933263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6933489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6941332	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs706860	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73524557	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73526655	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73526665	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7762181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7762977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7766150	1.00[CEU][hapmap]
rs7772508	1.00[CHB][hapmap]
rs785401	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs785403	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs785404	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs810826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs811484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs813068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9375015	0.86[AFR][1000 genomes]
rs9375017	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9385188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9385191	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9387932	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121575000-121606400	Weak transcription	NH-A	brain
2	chr6:121581000-121589200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:121582000-121588400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:121582000-121589000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:121582200-121603400	Weak transcription	HSMMtube	muscle
6	chr6:121582400-121588400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:121582400-121590400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:121582600-121588400	Weak transcription	Gastric	stomach
9	chr6:121582600-121588400	Weak transcription	Left Ventricle	heart
10	chr6:121585400-121590400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:121585400-121614200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:121585600-121588800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:121585600-121625000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:121585800-121588400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:121585800-121599000	Weak transcription	Primary B cells from cord blood	blood
16	chr6:121586400-121655000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:121586600-121588400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:121586600-121613000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:121587600-121588400	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:121587800-121588400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:121587800-121589000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:121587800-121589000	ZNF genes & repeats	Ovary	ovary
23	chr6:121587800-121589200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:121587800-121589200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr6:121588000-121588600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:121588000-121588600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr6:121588000-121588800	ZNF genes & repeats	Aorta	Aorta
28	chr6:121588000-121589000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:121588000-121589000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr6:121588000-121589000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr6:121588000-121589200	ZNF genes & repeats	Placenta	Placenta
32	chr6:121588000-121589200	ZNF genes & repeats	Fetal Stomach	stomach
33	chr6:121588000-121589200	ZNF genes & repeats	Pancreas	Pancrea
34	chr6:121588200-121588600	ZNF genes & repeats	Fetal Intestine Large	intestine
35	chr6:121588200-121588800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:121588200-121589000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr6:121588200-121589200	ZNF genes & repeats	Lung	lung
38	chr6:121588200-121589200	ZNF genes & repeats	Dnd41	blood
39	chr6:121588200-121589400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:121588200-121592000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:121588200-121616800	Weak transcription	Primary T cells from cord blood	blood

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