Variant report

Variant	rs11962214
Chromosome Location	chr6:128540348-128540349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10485161	1.00[CHB][hapmap]
rs10485162	1.00[CHB][hapmap]
rs10499137	1.00[JPT][hapmap]
rs10499138	1.00[JPT][hapmap]
rs10872329	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11961776	1.00[JPT][hapmap]
rs11962916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs11965115	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11967302	0.89[ASN][1000 genomes]
rs11968433	1.00[CHB][hapmap]
rs11970637	1.00[CHB][hapmap]
rs12110357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12110728	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1339188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1538498	1.00[CEU][hapmap]
rs1543376	1.00[CEU][hapmap]
rs17053270	1.00[CHB][hapmap]
rs17055270	1.00[JPT][hapmap]
rs17055274	1.00[JPT][hapmap]
rs17055391	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17055412	1.00[JPT][hapmap]
rs17055421	1.00[JPT][hapmap]
rs17055441	0.90[YRI][hapmap]
rs17055443	0.80[ASN][1000 genomes]
rs17055445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17055450	1.00[CEU][hapmap]
rs17055452	1.00[CEU][hapmap]
rs17055488	1.00[CHB][hapmap]
rs17055499	1.00[CHB][hapmap]
rs17055501	1.00[CHB][hapmap]
rs17055507	1.00[CHB][hapmap]
rs17055628	1.00[CEU][hapmap]
rs17055630	1.00[CEU][hapmap]
rs17055679	1.00[CEU][hapmap]
rs1738273	1.00[CHB][hapmap]
rs1738283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1738288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1738290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1768346	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1768347	1.00[CEU][hapmap]
rs1768353	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1768357	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1768358	1.00[CHB][hapmap]
rs1856498	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813371	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3813373	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3923033	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4072328	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs41439546	1.00[JPT][hapmap]
rs4440487	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4496822	1.00[JPT][hapmap]
rs4498385	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4895830	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4897244	1.00[JPT][hapmap]
rs4897245	1.00[JPT][hapmap]
rs4897246	1.00[JPT][hapmap]
rs4897247	1.00[JPT][hapmap]
rs4897248	1.00[JPT][hapmap]
rs4897250	1.00[JPT][hapmap]
rs6900798	1.00[CHB][hapmap]
rs6904354	0.89[ASN][1000 genomes]
rs6905735	1.00[CHB][hapmap]
rs6910587	1.00[CHB][hapmap]
rs6913718	1.00[CEU][hapmap]
rs6913738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs6918772	1.00[JPT][hapmap]
rs6928143	1.00[CEU][hapmap]
rs6929623	1.00[JPT][hapmap]
rs6933133	1.00[CHB][hapmap]
rs6935188	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6938118	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs6938199	1.00[JPT][hapmap]
rs73586607	0.89[ASN][1000 genomes]
rs73586609	0.89[ASN][1000 genomes]
rs73586611	0.89[ASN][1000 genomes]
rs73586613	0.89[ASN][1000 genomes]
rs73588647	0.89[ASN][1000 genomes]
rs73588698	0.80[ASN][1000 genomes]
rs73590658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746783	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7751187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7753945	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7754321	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754637	1.00[CHB][hapmap]
rs7755836	1.00[CEU][hapmap]
rs7768121	1.00[JPT][hapmap]
rs7769070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7772200	1.00[JPT][hapmap]
rs7772941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7773849	1.00[CEU][hapmap]
rs7776405	1.00[CEU][hapmap]
rs9375550	0.91[YRI][hapmap]
rs9388619	0.82[AFR][1000 genomes]
rs9388621	0.86[YRI][hapmap]
rs9388626	1.00[CEU][hapmap]
rs9398866	0.86[YRI][hapmap]
rs9402024	1.00[CEU][hapmap]
rs9784880	1.00[CEU][hapmap]
rs981998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv604647	chr6:128421762-128547177	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128503200-128541800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:128505800-128552200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:128523800-128540600	Weak transcription	Lung	lung
9	chr6:128523800-128543600	Weak transcription	Left Ventricle	heart
10	chr6:128526800-128541200	Weak transcription	Adipose Nuclei	Adipose
11	chr6:128527000-128543600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
13	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
15	chr6:128529400-128552600	Weak transcription	Small Intestine	intestine
16	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:128530000-128542000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:128531000-128550600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
20	chr6:128531200-128540400	Weak transcription	Pancreas	Pancrea
21	chr6:128531200-128554600	Weak transcription	Right Ventricle	heart
22	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
23	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:128531400-128543200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:128531400-128553600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:128532000-128545600	Weak transcription	NHEK	skin
28	chr6:128532000-128554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:128532000-128561000	Weak transcription	Osteobl	bone
30	chr6:128532200-128553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:128534400-128542200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:128535600-128543400	Weak transcription	Stomach Mucosa	stomach
33	chr6:128536000-128554800	Weak transcription	Brain Substantia Nigra	brain
34	chr6:128536800-128541200	Weak transcription	Placenta	Placenta
35	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
36	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:128537400-128543600	Weak transcription	Gastric	stomach
38	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:128538000-128540400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:128538200-128540400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:128538200-128540400	Strong transcription	Fetal Thymus	thymus
42	chr6:128538200-128540400	Strong transcription	HSMM	muscle
43	chr6:128538200-128540600	Strong transcription	Fetal Intestine Large	intestine
44	chr6:128538200-128540800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:128538600-128541200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:128538800-128540600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:128539000-128540400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:128539200-128541000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:128539600-128541000	Strong transcription	Primary B cells from cord blood	blood
50	chr6:128539800-128540400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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