Variant report

Variant	rs9382246
Chromosome Location	chr6:53715917-53715918
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53714815..53716814-chr6:53717074..53718725,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10755766	0.88[AMR][1000 genomes]
rs1076701	0.94[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes]
rs1076702	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes]
rs10948775	0.88[AMR][1000 genomes]
rs2073020	0.82[AMR][1000 genomes]
rs2294789	0.81[EUR][1000 genomes]
rs2294790	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2294791	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3777661	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4314499	0.90[AMR][1000 genomes]
rs4400206	0.83[TSI][hapmap]
rs4516937	0.83[TSI][hapmap]
rs4624872	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6903399	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906921	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6907027	0.86[CHB][hapmap]
rs6921605	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7751036	0.81[CHB][hapmap]
rs7763482	0.83[TSI][hapmap]
rs9349685	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357776	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes]
rs9370233	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370241	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9370244	0.82[AMR][1000 genomes]
rs9382232	0.88[AMR][1000 genomes]
rs9382233	0.88[AMR][1000 genomes]
rs9382235	0.85[YRI][hapmap]
rs9382238	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382241	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9382243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382248	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9382252	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382253	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382254	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382256	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9382257	0.92[AMR][1000 genomes]
rs9395876	0.88[AMR][1000 genomes]
rs9395878	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9395881	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9382246	ZNF451	cis	parietal	SCAN
rs9382246	HMGCLL1	cis	parietal	SCAN
rs9382246	LRRC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
3	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
7	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
8	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
9	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
10	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:53705400-53718800	Weak transcription	NHEK	skin
13	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
14	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:53707600-53718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:53707800-53718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53709400-53718600	Weak transcription	Gastric	stomach
20	chr6:53709600-53719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53709800-53719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
23	chr6:53710400-53720400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:53711200-53718800	Weak transcription	Fetal Intestine Large	intestine
25	chr6:53711200-53719800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:53711200-53720400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:53711400-53719600	Weak transcription	Thymus	Thymus
28	chr6:53712600-53720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:53712800-53719600	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:53712800-53720000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:53712800-53721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53713000-53717200	Weak transcription	Brain Substantia Nigra	brain
33	chr6:53713000-53719000	Weak transcription	Primary T cells from cord blood	blood
34	chr6:53713000-53719800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:53713000-53719800	Weak transcription	Fetal Thymus	thymus
36	chr6:53713000-53720000	Weak transcription	Brain Anterior Caudate	brain
37	chr6:53713000-53720200	Weak transcription	Dnd41	blood
38	chr6:53713000-53722000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:53713200-53719800	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:53713200-53720000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:53713400-53718400	Weak transcription	HepG2	liver
42	chr6:53715600-53716000	Enhancers	Fetal Intestine Small	intestine
43	chr6:53715600-53716400	Enhancers	Brain Angular Gyrus	brain
44	chr6:53715800-53716200	Weak transcription	Rectal Mucosa Donor 31	rectum

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