Variant report

Variant	rs978636
Chromosome Location	chr11:8836596-8836597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCC1	chr11:8835309-8836596	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr11:8835132-8836749	MCF10A-Er-Src	breast:	n/a	chr11:8836535-8836543 chr11:8836721-8836733 chr11:8836532-8836546 chr11:8836505-8836513
3	STAT1	chr11:8835157-8836788	Hela-S3	cervix:	n/a	chr11:8836535-8836543 chr11:8836533-8836544 chr11:8836721-8836733 chr11:8836532-8836546 chr11:8836505-8836513 chr11:8836506-8836517
4	STAT3	chr11:8835182-8836806	MCF10A-Er-Src	breast:	n/a	chr11:8836535-8836543 chr11:8836721-8836733 chr11:8836532-8836546 chr11:8836505-8836513
5	POLR2A	chr11:8836103-8836625	SK-N-MC	brain:	n/a	n/a
6	STAT3	chr11:8835128-8836787	MCF10A-Er-Src	breast:	n/a	chr11:8836535-8836543 chr11:8836721-8836733 chr11:8836532-8836546 chr11:8836505-8836513
7	POLR2A	chr11:8835148-8836616	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr11:8836489-8836701	MCF10A-Er-Src	breast:	n/a	chr11:8836535-8836543 chr11:8836532-8836546 chr11:8836505-8836513
9	MYC	chr11:8835150-8836678	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr11:8835199-8836639	MCF10A-Er-Src	breast:	n/a	chr11:8836573-8836587
11	FOS	chr11:8835145-8836760	MCF10A-Er-Src	breast:	n/a	chr11:8836573-8836587
12	CTCF	chr11:8836580-8836730	WI-38	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8711214..8713494-chr11:8834662..8837467,3	K562	blood:
2	chr11:8707625..8713219-chr11:8836057..8840145,5	K562	blood:
3	chr11:8835358..8837463-chr11:8838521..8841389,2	MCF-7	breast:
4	chr11:8708964..8711177-chr11:8835969..8837619,2	MCF-7	breast:
5	chr11:8836156..8836984-chr11:60928785..60929437,2	Hela-S3	cervix:
6	chr11:8707625..8711209-chr11:8836057..8839950,3	K562	blood:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000167987	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10743093	0.86[EUR][1000 genomes]
rs10769967	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10769968	0.82[EUR][1000 genomes]
rs10769970	0.80[EUR][1000 genomes]
rs10769971	0.80[EUR][1000 genomes]
rs10769973	0.80[EUR][1000 genomes]
rs10840130	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10840134	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840141	0.81[EUR][1000 genomes]
rs10840142	0.82[EUR][1000 genomes]
rs10840147	0.80[EUR][1000 genomes]
rs10840148	0.80[EUR][1000 genomes]
rs11042078	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042079	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042082	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042088	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042102	0.84[EUR][1000 genomes]
rs11042103	0.83[EUR][1000 genomes]
rs11603841	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794444	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529641	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1569408	0.82[EUR][1000 genomes]
rs1883098	0.82[EUR][1000 genomes]
rs1988708	0.82[EUR][1000 genomes]
rs1988709	0.84[EUR][1000 genomes]
rs2568043	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568054	0.82[EUR][1000 genomes]
rs2568059	0.84[EUR][1000 genomes]
rs2568061	0.83[EUR][1000 genomes]
rs2568062	0.83[EUR][1000 genomes]
rs2568065	0.82[EUR][1000 genomes]
rs2568090	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653567	0.82[EUR][1000 genomes]
rs2653593	0.83[EUR][1000 genomes]
rs2653606	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2653607	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653616	0.83[EUR][1000 genomes]
rs2742550	0.83[EUR][1000 genomes]
rs34842234	0.83[EUR][1000 genomes]
rs3763918	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4554887	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910062	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61876187	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7107867	0.81[AMR][1000 genomes]
rs7119939	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7123429	0.88[EUR][1000 genomes]
rs7123861	0.84[EUR][1000 genomes]
rs7937298	0.88[EUR][1000 genomes]
rs7943377	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527073	chr11:8829168-8848463	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs978636	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs978636	TMEM9B-AS1	cis	lung	GTEx
rs978636	AKIP1	cis	Thyroid	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8832400-8836800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr11:8832600-8840800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:8832800-8837400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:8833000-8837200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:8833000-8837200	Enhancers	NHDF-Ad	bronchial
6	chr11:8833000-8837400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:8833000-8837600	Enhancers	NHLF	lung
8	chr11:8833000-8839200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:8833200-8836600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:8833200-8837000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr11:8833200-8837000	Weak transcription	Esophagus	oesophagus
12	chr11:8833200-8837200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:8833200-8837200	Enhancers	HMEC	breast
14	chr11:8833200-8837200	Enhancers	Osteobl	bone
15	chr11:8833200-8837400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:8833200-8837400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:8833200-8837400	Enhancers	NHEK	skin
18	chr11:8833200-8837800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
20	chr11:8833400-8837200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:8833800-8837400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr11:8834000-8836600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:8834200-8837400	Enhancers	Placenta	Placenta
24	chr11:8834200-8838600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:8834200-8839000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:8834400-8836600	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr11:8834400-8837400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:8834600-8837400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:8834800-8837000	Flanking Active TSS	Hela-S3	cervix
30	chr11:8834800-8837400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr11:8834800-8837400	Enhancers	Dnd41	blood
32	chr11:8834800-8838200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:8835000-8836600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:8835000-8836600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:8835000-8836800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:8835000-8837000	Enhancers	Fetal Thymus	thymus
37	chr11:8835000-8837000	Enhancers	NH-A	brain
38	chr11:8835000-8837200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr11:8835000-8837200	Enhancers	HSMMtube	muscle
40	chr11:8835000-8837400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:8835200-8837200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:8835200-8837800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:8835400-8836600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:8835400-8836600	Enhancers	Fetal Lung	lung
45	chr11:8835400-8836600	Enhancers	Spleen	Spleen
46	chr11:8835400-8836800	Enhancers	Ovary	ovary
47	chr11:8835400-8837200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr11:8835400-8837200	Enhancers	Fetal Kidney	kidney
49	chr11:8835400-8837600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr11:8835600-8836600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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