Variant report

Variant	rs11964671
Chromosome Location	chr6:37798804-37798805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37797940..37799807-chr6:37808764..37811623,2	MCF-7	breast:
2	chr6:37797639..37800200-chr6:37805960..37807518,2	K562	blood:
3	chr6:37786464..37788426-chr6:37798641..37800200,2	K562	blood:
4	chr6:37784606..37792959-chr6:37792982..37799004,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11752809	0.87[ASN][1000 genomes]
rs11752814	0.87[ASN][1000 genomes]
rs11753300	0.87[ASN][1000 genomes]
rs11759458	1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs11964613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968604	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970145	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190751	0.87[ASN][1000 genomes]
rs13198459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13200310	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13203867	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13205214	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13207526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210967	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13211881	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890185	1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[ASN][1000 genomes]
rs16890194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16890301	0.88[CEU][hapmap]
rs2103950	0.96[ASN][1000 genomes]
rs2395689	0.88[CEU][hapmap]
rs2453882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2645104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs2645115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2645118	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2645121	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2645123	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2645126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2842498	1.00[AMR][1000 genomes]
rs2842499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842506	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842511	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2842512	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842513	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34011349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054102	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34611895	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745343	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35248825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35330991	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35379375	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35609407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35653300	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35849984	0.84[ASN][1000 genomes]
rs35953900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35955196	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36069529	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4394213	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56391784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458037	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6908106	1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs6908761	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6910715	0.82[JPT][hapmap]
rs6910837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6911481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6912250	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6918802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919884	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923132	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6925563	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933547	1.00[YRI][hapmap]
rs6936260	0.82[JPT][hapmap]
rs6940491	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71569395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7742379	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7747538	0.84[AMR][1000 genomes]
rs7750445	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7760770	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762052	0.82[JPT][hapmap]
rs7776025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers 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
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37789400-37800000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr6:37790800-37799200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:37791000-37799200	Weak transcription	Esophagus	oesophagus
4	chr6:37791000-37800400	Weak transcription	Thymus	Thymus
5	chr6:37791200-37800000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:37791400-37799200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:37791400-37799200	Weak transcription	Pancreas	Pancrea
9	chr6:37791400-37799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:37791400-37799400	Weak transcription	Aorta	Aorta
11	chr6:37791400-37800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:37791400-37800400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:37791400-37801800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:37791400-37801800	Weak transcription	Fetal Brain Female	brain
15	chr6:37791400-37801800	Weak transcription	A549	lung
16	chr6:37791400-37810200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:37791600-37799200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:37791600-37800000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:37791600-37801400	Weak transcription	Brain Germinal Matrix	brain
22	chr6:37792000-37800400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:37792400-37800400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:37792400-37801800	Weak transcription	Fetal Brain Male	brain
25	chr6:37793200-37799000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:37793800-37801600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:37793800-37813600	Weak transcription	NH-A	brain
28	chr6:37794000-37819800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:37794400-37799000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:37794400-37799200	Weak transcription	Placenta	Placenta
31	chr6:37794400-37805200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:37794600-37799200	Enhancers	Dnd41	blood
33	chr6:37794800-37800800	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:37795000-37813800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:37795000-37825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:37795200-37799800	Weak transcription	HepG2	liver
37	chr6:37795400-37799600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:37795800-37799000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:37795800-37799000	Weak transcription	K562	blood
40	chr6:37795800-37799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:37795800-37799200	Weak transcription	Lung	lung
42	chr6:37795800-37802200	Weak transcription	NHLF	lung
43	chr6:37795800-37813400	Weak transcription	HSMMtube	muscle
44	chr6:37796000-37799200	Weak transcription	Left Ventricle	heart
45	chr6:37796000-37799200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:37796000-37800400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:37796000-37800400	Weak transcription	Fetal Stomach	stomach
48	chr6:37796000-37800600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:37796000-37812800	Weak transcription	Colonic Mucosa	Colon
50	chr6:37796000-37813200	Weak transcription	Rectal Mucosa Donor 29	rectum

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