Variant report

Variant	rs11235594
Chromosome Location	chr11:72503735-72503736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72502078..72507217-chr11:72523813..72527208,9	K562	blood:
2	chr11:72432212..72438079-chr11:72503579..72507160,8	MCF-7	breast:
3	chr11:72487526..72509577-chr11:72522325..72536312,93	MCF-7	breast:
4	chr11:72503176..72507418-chr11:72523751..72527635,5	MCF-7	breast:
5	chr11:72502776..72504800-chr11:72523813..72526790,2	K562	blood:
6	chr11:72433323..72435429-chr11:72502768..72506514,3	K562	blood:
7	chr11:72462706..72465111-chr11:72501934..72505822,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186635	Chromatin interaction
ENSG00000168010	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1000620	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431171	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431172	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10431174	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10751213	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10751215	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10751216	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898877	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898879	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898880	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10898881	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs11235592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235596	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864653	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975109	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35343925	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35668754	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35752694	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4459331	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4459332	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485099	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944797	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944800	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944802	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944805	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6592486	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592489	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592490	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110719	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7952617	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	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
3	nsv825992	chr11:72476174-72524295	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11235594	STARD10	cis	Whole Blood	GTEx
rs11235594	ARHGEF17	cis	cerebellum	SCAN
rs11235594	FGF4	cis	cerebellum	SCAN
rs11235594	STARD10	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72493800-72504200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:72493800-72504200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:72494000-72504400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:72494000-72504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:72498800-72503800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:72498800-72504200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:72499000-72504000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:72499000-72504000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:72499000-72504400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:72499400-72504400	Weak transcription	Pancreas	Pancrea
11	chr11:72499600-72503800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:72500600-72504000	Enhancers	Fetal Brain Male	brain
13	chr11:72500800-72504000	Weak transcription	Small Intestine	intestine
14	chr11:72500800-72504800	Weak transcription	Psoas Muscle	Psoas
15	chr11:72501000-72503800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:72501000-72503800	Weak transcription	Adipose Nuclei	Adipose
17	chr11:72501000-72504000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:72501000-72504000	Weak transcription	A549	lung
19	chr11:72501000-72504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:72501000-72504600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:72501200-72503800	Weak transcription	Fetal Stomach	stomach
22	chr11:72501200-72503800	Weak transcription	HSMM	muscle
23	chr11:72501200-72504800	Weak transcription	Gastric	stomach
24	chr11:72501400-72503800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:72501400-72503800	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:72501400-72503800	Weak transcription	Placenta	Placenta
27	chr11:72501400-72504000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:72501400-72504000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:72501400-72504200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:72501400-72504200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:72501400-72504200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:72501400-72504200	Weak transcription	HMEC	breast
33	chr11:72501400-72504200	Weak transcription	NHLF	lung
34	chr11:72501400-72504400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:72501400-72504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:72501400-72504400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:72501600-72503800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:72501600-72504200	Weak transcription	NHEK	skin
39	chr11:72501800-72503800	Weak transcription	Left Ventricle	heart
40	chr11:72501800-72504200	Weak transcription	NH-A	brain
41	chr11:72502000-72504000	Weak transcription	Osteobl	bone
42	chr11:72502000-72504400	Weak transcription	Ovary	ovary
43	chr11:72502200-72504000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr11:72502400-72503800	Weak transcription	Stomach Mucosa	stomach
45	chr11:72502400-72504400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:72502600-72503800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:72503200-72503800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:72503200-72504200	Enhancers	Primary B cells from cord blood	blood
49	chr11:72503200-72504200	Enhancers	Primary T cells fromperipheralblood	blood
50	chr11:72503200-72504400	Enhancers	Primary T helper cells fromperipheralblood	blood

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