Variant report

Variant	rs7119939
Chromosome Location	chr11:8861543-8861544
allele	G/T
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	RELA	chr11:8861260-8861886	GM12878	blood:	n/a	chr11:8861627-8861636 chr11:8861627-8861636
2	POLR2A	chr11:8861173-8862388	H1-hESC	embryonic stem cell:	n/a	n/a
3	IKZF1	chr11:8861297-8861740	GM12878	blood:	n/a	n/a
4	SP1	chr11:8861401-8861973	H1-hESC	embryonic stem cell:	n/a	chr11:8861633-8861642
5	MAX	chr11:8861531-8862006	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr11:8861541-8862055	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOS	chr11:8861443-8861756	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr11:8861543-8861814	HUVEC	blood vessel:	n/a	n/a
9	RELA	chr11:8861426-8861818	GM19099	blood:	n/a	chr11:8861627-8861636 chr11:8861627-8861636
10	POLR2A	chr11:8861382-8861991	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:8861515-8861917	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT3	chr11:8861374-8861648	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA2	chr11:8861480-8861885	A549	lung:	n/a	n/a
14	TCF12	chr11:8861519-8861807	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOXA1	chr11:8861388-8861802	HepG2	liver:	n/a	chr11:8861679-8861694
16	FOS	chr11:8861451-8861725	MCF10A-Er-Src	breast:	n/a	n/a
17	FOXA1	chr11:8861537-8861831	HepG2	liver:	n/a	chr11:8861679-8861694
18	FOXA1	chr11:8861462-8861924	HepG2	liver:	n/a	chr11:8861679-8861694
19	FOXA1	chr11:8861510-8861869	HepG2	liver:	n/a	chr11:8861679-8861694
20	ATF2	chr11:8861458-8861927	H1-hESC	embryonic stem cell:	n/a	n/a
21	RELA	chr11:8861192-8861820	GM18951	blood:	n/a	chr11:8861627-8861636 chr11:8861627-8861636
22	STAT3	chr11:8861416-8861758	MCF10A-Er-Src	breast:	n/a	n/a
23	GTF2F1	chr11:8861543-8861837	H1-hESC	embryonic stem cell:	n/a	n/a
24	RELA	chr11:8860978-8862118	GM12891	blood:	n/a	chr11:8861627-8861636 chr11:8861627-8861636
25	POLR2A	chr11:8861038-8862444	H1-hESC	embryonic stem cell:	n/a	n/a
26	EP300	chr11:8861399-8861956	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZNF143	chr11:8861059-8862358	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXA2	chr11:8861461-8861827	A549	lung:	n/a	n/a
29	NFIC	chr11:8861363-8861787	GM12878	blood:	n/a	n/a
30	RCOR1	chr11:8859305-8862295	IMR90	lung:	n/a	n/a
31	TAF1	chr11:8861543-8861941	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOXA2	chr11:8861503-8861802	HepG2	liver:	n/a	n/a
33	CTBP2	chr11:8861134-8862473	H1-hESC	embryonic stem cell:	n/a	n/a
34	RUNX3	chr11:8861439-8861998	GM12878	blood:	n/a	chr11:8861877-8861886
35	RELA	chr11:8861381-8861997	GM19193	blood:	n/a	chr11:8861627-8861636 chr11:8861627-8861636
36	YY1	chr11:8861399-8862134	H1-hESC	embryonic stem cell:	n/a	n/a
37	SP1	chr11:8861433-8861911	H1-hESC	embryonic stem cell:	n/a	chr11:8861633-8861642
38	EBF1	chr11:8861383-8861959	GM12878	blood:	n/a	chr11:8861436-8861446 chr11:8861436-8861445

Variant related genes	Relation type
ST5	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10743093	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769967	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769968	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769970	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10769971	0.80[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10769973	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10769979	0.92[CEU][hapmap]
rs10840130	0.88[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840141	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840142	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840147	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840148	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042078	0.92[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11042079	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11042082	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042088	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042102	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042103	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042125	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11042151	0.92[CEU][hapmap]
rs11042154	0.92[CEU][hapmap]
rs1123936	0.84[CEU][hapmap]
rs11603841	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12224436	0.80[CEU][hapmap]
rs12794444	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1529641	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1560569	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1569408	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1883098	0.84[EUR][1000 genomes]
rs1980428	0.84[CEU][hapmap]
rs1980429	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1988708	0.84[EUR][1000 genomes]
rs1988709	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2016942	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2568043	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2568045	0.84[CEU][hapmap]
rs2568054	0.84[EUR][1000 genomes]
rs2568059	0.85[EUR][1000 genomes]
rs2568061	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2568062	0.84[EUR][1000 genomes]
rs2568065	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2568090	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653567	0.84[EUR][1000 genomes]
rs2653570	0.80[CEU][hapmap]
rs2653593	0.85[EUR][1000 genomes]
rs2653605	0.84[CEU][hapmap]
rs2653606	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653607	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653616	0.85[EUR][1000 genomes]
rs2742480	0.84[CEU][hapmap]
rs2742536	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs2742537	0.84[CEU][hapmap]
rs2742540	0.88[CEU][hapmap]
rs2742545	0.88[CEU][hapmap]
rs2742550	0.85[EUR][1000 genomes]
rs2742552	0.88[CEU][hapmap]
rs34842234	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4554887	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4909952	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4910062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910119	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910442	0.84[CEU][hapmap]
rs4929922	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs61876187	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486060	0.84[CEU][hapmap]
rs7123429	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7123861	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7479407	0.92[CEU][hapmap]
rs7925728	0.92[CEU][hapmap]
rs7930026	0.96[CEU][hapmap]
rs7937298	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7943377	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7945705	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs978636	0.85[AMR][1000 genomes];0.96[EUR][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	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7119939	AKIP1	cis	Thyroid	GTEx
rs7119939	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs7119939	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8851800-8862400	Enhancers	Placenta	Placenta
2	chr11:8852800-8861600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8855400-8861800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:8855800-8861600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:8858600-8862600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:8859200-8862400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:8859200-8862400	Enhancers	NHLF	lung
8	chr11:8859200-8862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:8859200-8862600	Enhancers	Fetal Lung	lung
10	chr11:8859200-8862600	Enhancers	Small Intestine	intestine
11	chr11:8859400-8862400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:8859400-8862400	Enhancers	Ovary	ovary
13	chr11:8859400-8862400	Enhancers	Right Atrium	heart
14	chr11:8859400-8862400	Enhancers	Stomach Mucosa	stomach
15	chr11:8859400-8862400	Enhancers	Spleen	Spleen
16	chr11:8859400-8862400	Enhancers	HSMMtube	muscle
17	chr11:8859400-8862600	Enhancers	HMEC	breast
18	chr11:8859400-8864000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:8859600-8862000	Enhancers	Adipose Nuclei	Adipose
20	chr11:8859600-8862400	Enhancers	Fetal Stomach	stomach
21	chr11:8859600-8862400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr11:8859600-8863000	Enhancers	Fetal Muscle Leg	muscle
23	chr11:8859800-8861800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:8859800-8862200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:8859800-8862400	Enhancers	Colon Smooth Muscle	Colon
26	chr11:8859800-8862400	Enhancers	Rectal Smooth Muscle	rectum
27	chr11:8859800-8862600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:8859800-8862600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr11:8859800-8862600	Enhancers	Duodenum Mucosa	Duodenum
30	chr11:8859800-8862600	Enhancers	Fetal Kidney	kidney
31	chr11:8859800-8863200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:8859800-8863800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr11:8860000-8862400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr11:8860000-8862400	Enhancers	Right Ventricle	heart
35	chr11:8860000-8862600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:8860000-8862800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:8860000-8863200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:8860200-8861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:8860200-8861600	Weak transcription	HSMM	muscle
40	chr11:8860200-8862200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:8860200-8862400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:8860200-8862400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr11:8860200-8862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:8860200-8862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:8860200-8863400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:8860400-8861800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:8860400-8862000	Enhancers	NHDF-Ad	bronchial
48	chr11:8860400-8862400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:8860400-8862400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:8860400-8862400	Enhancers	Gastric	stomach

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