Variant report

Variant	rs4910062
Chromosome Location	chr11:8862188-8862189
allele	A/C
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	POLR2A	chr11:8861173-8862388	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr11:8861903-8862203	PFSK-1	brain:	n/a	chr11:8861999-8862019
3	REST	chr11:8861819-8862287	ECC-1	luminal epithelium:	n/a	chr11:8861999-8862019
4	POLR2A	chr11:8861038-8862444	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr11:8861777-8862265	PANC-1	pancreas:	n/a	chr11:8861999-8862019
6	REST	chr11:8861838-8862273	ECC-1	luminal epithelium:	n/a	chr11:8861999-8862019
7	POLR2A	chr11:8862177-8862391	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr11:8861849-8862232	H1-hESC	embryonic stem cell:	n/a	chr11:8861999-8862019
9	RFX5	chr11:8861974-8862200	HepG2	liver:	n/a	chr11:8862037-8862052
10	ZNF143	chr11:8861059-8862358	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr11:8861825-8862225	PFSK-1	brain:	n/a	chr11:8861999-8862019
12	RCOR1	chr11:8859305-8862295	IMR90	lung:	n/a	n/a
13	CTBP2	chr11:8861134-8862473	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr11:8861828-8862197	H1-hESC	embryonic stem cell:	n/a	chr11:8861999-8862019

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8854948..8856517-chr11:8861568..8863315,2	MCF-7	breast:
2	chr11:8850578..8853466-chr11:8861792..8863459,2	K562	blood:

Variant related genes	Relation type
RNA5SP330	TF binding region
ST5	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769955	1.00[YRI][hapmap]
rs10769957	1.00[YRI][hapmap]
rs10769967	1.00[CEU][hapmap];0.85[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10769971	0.84[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10769979	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs10840114	1.00[YRI][hapmap]
rs10840130	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840134	1.00[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042059	1.00[YRI][hapmap]
rs11042069	1.00[YRI][hapmap]
rs11042078	1.00[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042125	0.90[JPT][hapmap]
rs11042151	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs11042154	0.92[CEU][hapmap]
rs1123936	0.83[CEU][hapmap]
rs11603841	0.96[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];0.84[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1560569	0.92[CEU][hapmap];0.85[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	0.83[CEU][hapmap]
rs1980429	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs1984791	1.00[YRI][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];0.90[JPT][hapmap]
rs2316865	1.00[YRI][hapmap]
rs2568043	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2568045	0.83[CEU][hapmap]
rs2568054	0.84[EUR][1000 genomes]
rs2568059	0.85[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs2568062	0.84[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653567	0.84[EUR][1000 genomes]
rs2653570	0.80[JPT][hapmap]
rs2653593	0.85[EUR][1000 genomes]
rs2653605	0.83[CEU][hapmap];0.80[JPT][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	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs2742536	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs2742537	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs2742540	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2742545	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs2742550	0.85[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap];0.81[CHB][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];0.89[JPT][hapmap]
rs4910119	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4929922	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs61876187	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486060	0.83[CEU][hapmap]
rs7119939	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]
rs7123429	1.00[CEU][hapmap];0.81[CHB][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];0.80[JPT][hapmap]
rs7925728	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs7930026	0.92[CEU][hapmap]
rs7937298	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7940366	1.00[YRI][hapmap]
rs7943377	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7945705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7947631	0.84[CEU][hapmap]
rs905290	1.00[YRI][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
rs4910062	AKIP1	cis	Thyroid	GTEx
rs4910062	TMEM9B-AS1	cis	lung	GTEx
rs4910062	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8851800-8862400	Enhancers	Placenta	Placenta
2	chr11:8858600-8862600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:8859200-8862400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:8859200-8862400	Enhancers	NHLF	lung
5	chr11:8859200-8862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr11:8859200-8862600	Enhancers	Fetal Lung	lung
7	chr11:8859200-8862600	Enhancers	Small Intestine	intestine
8	chr11:8859400-8862400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:8859400-8862400	Enhancers	Ovary	ovary
10	chr11:8859400-8862400	Enhancers	Right Atrium	heart
11	chr11:8859400-8862400	Enhancers	Stomach Mucosa	stomach
12	chr11:8859400-8862400	Enhancers	Spleen	Spleen
13	chr11:8859400-8862400	Enhancers	HSMMtube	muscle
14	chr11:8859400-8862600	Enhancers	HMEC	breast
15	chr11:8859400-8864000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:8859600-8862400	Enhancers	Fetal Stomach	stomach
17	chr11:8859600-8862400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr11:8859600-8863000	Enhancers	Fetal Muscle Leg	muscle
19	chr11:8859800-8862200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr11:8859800-8862400	Enhancers	Colon Smooth Muscle	Colon
21	chr11:8859800-8862400	Enhancers	Rectal Smooth Muscle	rectum
22	chr11:8859800-8862600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:8859800-8862600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr11:8859800-8862600	Enhancers	Duodenum Mucosa	Duodenum
25	chr11:8859800-8862600	Enhancers	Fetal Kidney	kidney
26	chr11:8859800-8863200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr11:8859800-8863800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr11:8860000-8862400	Enhancers	H9 Cell Line	embryonic stem cell
29	chr11:8860000-8862400	Enhancers	Right Ventricle	heart
30	chr11:8860000-8862600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr11:8860000-8862800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:8860000-8863200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:8860200-8862200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:8860200-8862400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:8860200-8862400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr11:8860200-8862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:8860200-8862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:8860200-8863400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:8860400-8862400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:8860400-8862400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:8860400-8862400	Enhancers	Gastric	stomach
42	chr11:8860400-8862600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:8860600-8862400	Enhancers	Fetal Thymus	thymus
44	chr11:8860600-8863600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr11:8860600-8864400	Weak transcription	Osteobl	bone
46	chr11:8861000-8862200	Enhancers	Fetal Intestine Small	intestine
47	chr11:8861000-8862400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:8861000-8862400	Enhancers	Esophagus	oesophagus
49	chr11:8861000-8862400	Enhancers	Left Ventricle	heart
50	chr11:8861000-8862400	Enhancers	Lung	lung

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