Variant report

Variant	rs735942
Chromosome Location	chr11:65749337-65749338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65486611..65489358-chr11:65749045..65751139,2	MCF-7	breast:
2	chr11:65748830..65750592-chr11:65753511..65756677,3	MCF-7	breast:
3	chr11:65749073..65751000-chr11:65779074..65782021,3	MCF-7	breast:
4	chr11:65628030..65631325-chr11:65748235..65751654,3	MCF-7	breast:
5	chr11:65748971..65751711-chr11:65753377..65755167,2	MCF-7	breast:
6	chr11:65739309..65741332-chr11:65747619..65750098,2	MCF-7	breast:
7	chr11:65748017..65751656-chr11:65762573..65766422,5	K562	blood:
8	chr11:65747825..65750124-chr11:65778940..65780987,2	MCF-7	breast:
9	chr11:65742158..65748813-chr11:65749011..65756801,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172922	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1047464	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791835	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10791837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896070	0.98[ASN][1000 genomes]
rs10896073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896074	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12363614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12576996	0.89[JPT][hapmap]
rs2276132	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759035	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55947178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60109456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6591195	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7128076	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs747526	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754532	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7939253	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9735063	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
3	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
8	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs735942	ESRRA	cis	cerebellum	SCAN
rs735942	EIF1AD	cis	parietal	SCAN
rs735942	BANF1	cis	multi-tissue	Pritchard
rs735942	BANF1	cis	Esophagus Mucosa	GTEx
rs735942	PYGM	cis	parietal	SCAN
rs735942	EFEMP2	cis	cerebellum	SCAN
rs735942	FADS3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
2	chr11:65731200-65749600	Strong transcription	Fetal Intestine Small	intestine
3	chr11:65735200-65750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:65735800-65756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
6	chr11:65737800-65756600	Weak transcription	Stomach Mucosa	stomach
7	chr11:65739200-65749600	Strong transcription	Fetal Brain Female	brain
8	chr11:65739600-65756400	Weak transcription	Fetal Kidney	kidney
9	chr11:65739800-65756400	Weak transcription	Hela-S3	cervix
10	chr11:65741200-65765000	Weak transcription	NHDF-Ad	bronchial
11	chr11:65741400-65762000	Weak transcription	HSMMtube	muscle
12	chr11:65741600-65762000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:65742200-65759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:65743000-65749400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:65743800-65764800	Weak transcription	HSMM	muscle
16	chr11:65745000-65764200	Weak transcription	HUVEC	blood vessel
17	chr11:65745200-65764800	Weak transcription	K562	blood
18	chr11:65745400-65750800	Weak transcription	HepG2	liver
19	chr11:65745400-65764800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:65745400-65765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:65745600-65764200	Weak transcription	NH-A	brain
22	chr11:65745800-65756600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr11:65745800-65764800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:65746000-65764600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:65746800-65756400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:65746800-65765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:65747000-65756400	Weak transcription	Primary B cells from cord blood	blood
28	chr11:65747000-65756400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:65747000-65756400	Weak transcription	Aorta	Aorta
30	chr11:65747000-65756400	Weak transcription	Colon Smooth Muscle	Colon
31	chr11:65747000-65764200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:65747000-65764600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:65747000-65764600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:65747000-65764600	Weak transcription	Ovary	ovary
35	chr11:65747000-65764800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:65747200-65750200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr11:65747200-65750600	Weak transcription	NHLF	lung
38	chr11:65747200-65755600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:65747200-65756200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr11:65747200-65756400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr11:65747200-65756400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:65747200-65756400	Weak transcription	GM12878-XiMat	blood
43	chr11:65747200-65756600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:65747200-65757200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:65747200-65759800	Weak transcription	Lung	lung
46	chr11:65747200-65764200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:65747200-65764200	Weak transcription	Adipose Nuclei	Adipose
48	chr11:65747200-65764200	Weak transcription	Liver	Liver
49	chr11:65747200-65764200	Weak transcription	A549	lung
50	chr11:65747200-65764400	Weak transcription	Left Ventricle	heart

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