Variant report

Variant	rs11969346
Chromosome Location	chr6:166940783-166940784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11961008	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11961547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962002	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962046	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962068	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962104	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962129	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962190	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962191	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962250	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967122	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968034	0.90[YRI][hapmap]
rs11968040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969688	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11970138	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970162	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970189	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970312	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526968	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204765	0.84[AFR][1000 genomes]
rs17505698	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17584003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33973677	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007078	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778423	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799649	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs57672678	0.94[EUR][1000 genomes]
rs6903112	0.81[AFR][1000 genomes]
rs6903487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908724	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908895	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923077	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923273	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73788006	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73788028	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs754491	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv605259	chr6:166936021-166952981	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
5	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
7	chr6:166921400-166943600	Weak transcription	Fetal Lung	lung
8	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:166923200-166943200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas
12	chr6:166923800-166953000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:166928800-166943400	Weak transcription	Fetal Brain Female	brain
14	chr6:166929000-166943400	Weak transcription	Liver	Liver
15	chr6:166929400-166943000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:166929600-166942800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:166929600-166954000	Weak transcription	HSMM	muscle
18	chr6:166929600-166955600	Weak transcription	HMEC	breast
19	chr6:166930200-166944000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:166930400-166943000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:166930400-166943800	Weak transcription	Esophagus	oesophagus
22	chr6:166930400-166954200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:166930600-166942800	Weak transcription	Brain Substantia Nigra	brain
25	chr6:166931600-166941600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:166931600-166943200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:166932000-166941400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr6:166932200-166941800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:166932400-166948600	Weak transcription	Primary B cells from cord blood	blood
30	chr6:166932600-166953800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:166933000-166942800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:166933200-166941600	Strong transcription	Lung	lung
33	chr6:166933200-166953200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:166933800-166953400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:166934400-166944000	Weak transcription	Fetal Intestine Large	intestine
36	chr6:166935200-166941600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:166935200-166941600	Strong transcription	Left Ventricle	heart
38	chr6:166935400-166952000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:166935400-166966400	Weak transcription	NH-A	brain
40	chr6:166935600-166943800	Weak transcription	Fetal Intestine Small	intestine
41	chr6:166936400-166943200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:166938000-166943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:166938200-166941200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:166938200-166948800	Weak transcription	HUVEC	blood vessel
45	chr6:166938200-166955800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:166938400-166943200	Weak transcription	HSMMtube	muscle
47	chr6:166938600-166940800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:166938600-166941600	Strong transcription	Osteobl	bone
49	chr6:166938600-166943200	Weak transcription	Pancreas	Pancrea
50	chr6:166939000-166942800	Weak transcription	Brain Hippocampus Middle	brain

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