Variant report

Variant	rs7946861
Chromosome Location	chr11:72557986-72557987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72550927..72553163-chr11:72557469..72559694,2	MCF-7	breast:
2	chr11:72554260..72556013-chr11:72557786..72559604,2	K562	blood:
3	chr11:72436394..72438545-chr11:72556788..72559198,2	K562	blood:
4	chr11:72547760..72550663-chr11:72556425..72558728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186635	Chromatin interaction
ENSG00000137478	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10793048	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898885	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898889	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11235620	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11822039	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12799445	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12805658	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12808517	0.84[CEU][hapmap]
rs3862794	0.84[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs3862796	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4400839	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs4944014	0.85[AMR][1000 genomes]
rs4944016	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519790	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs593753	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6592500	0.84[CEU][hapmap]
rs6592505	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs663015	0.84[CHB][hapmap]
rs7108955	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs7126070	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7946861	STARD10	cis	multi-tissue	Pritchard
rs7946861	ATG16L2	cis	parietal	SCAN
rs7946861	STARD10	cis	Whole Blood	GTEx
rs7946861	PDE2A	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72540200-72616600	Strong transcription	Primary B cells from peripheral blood	blood
2	chr11:72540600-72589800	Strong transcription	Primary B cells from cord blood	blood
3	chr11:72541600-72558400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:72543200-72558200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:72543200-72562200	Weak transcription	A549	lung
6	chr11:72543200-72614800	Weak transcription	Psoas Muscle	Psoas
7	chr11:72543400-72560800	Strong transcription	GM12878-XiMat	blood
8	chr11:72543400-72603000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:72545200-72561000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:72546000-72558000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:72546000-72558600	Strong transcription	Liver	Liver
12	chr11:72546600-72561000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:72546800-72559200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:72546800-72561400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:72547400-72561200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:72548000-72559600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:72548400-72561000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:72548400-72561000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:72549600-72558400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:72550000-72600400	Weak transcription	Pancreas	Pancrea
21	chr11:72551200-72563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:72552000-72567000	Weak transcription	NH-A	brain
23	chr11:72552200-72562000	Weak transcription	Esophagus	oesophagus
24	chr11:72552200-72575400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:72552200-72580400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:72552400-72597400	Weak transcription	HMEC	breast
27	chr11:72552800-72578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:72553400-72567000	Weak transcription	HUVEC	blood vessel
29	chr11:72553600-72576000	Weak transcription	NHEK	skin
30	chr11:72553800-72560600	Weak transcription	Gastric	stomach
31	chr11:72554400-72560000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:72554400-72560200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:72554400-72560200	Weak transcription	Placenta	Placenta
34	chr11:72554400-72564000	Weak transcription	Brain Germinal Matrix	brain
35	chr11:72554400-72567000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr11:72554400-72567000	Weak transcription	Adipose Nuclei	Adipose
37	chr11:72554400-72567200	Weak transcription	Brain Substantia Nigra	brain
38	chr11:72554400-72574200	Weak transcription	Aorta	Aorta
39	chr11:72554400-72576000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:72554600-72558400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:72554600-72559800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:72554600-72559800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:72554600-72560000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:72554600-72563200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:72554600-72567000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:72554600-72567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:72554600-72567800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:72554600-72568000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:72554600-72570600	Weak transcription	Colonic Mucosa	Colon
50	chr11:72554600-72577000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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