Variant report

Variant	rs2056903
Chromosome Location	chr11:8940149-8940150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8936222..8938105-chr11:8938810..8940330,2	MCF-7	breast:
2	chr11:8702949..8705431-chr11:8939246..8941790,2	K562	blood:
3	chr11:8932894..8935848-chr11:8939704..8942877,3	MCF-7	breast:
4	chr11:8714148..8716877-chr11:8938589..8940698,2	K562	blood:

Variant related genes	Relation type
ENSG00000166452	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000254665	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10219366	0.95[EUR][1000 genomes]
rs1025438	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10734639	0.91[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10743094	0.83[EUR][1000 genomes]
rs10769974	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs10769976	0.96[EUR][1000 genomes]
rs10769977	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10840150	0.87[EUR][1000 genomes]
rs10840151	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10840153	0.81[EUR][1000 genomes]
rs10840154	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840155	0.81[EUR][1000 genomes]
rs10840156	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11042121	0.88[EUR][1000 genomes]
rs11042131	0.81[EUR][1000 genomes]
rs1133833	0.81[MEX][hapmap]
rs1136966	0.86[MEX][hapmap]
rs12296005	0.85[JPT][hapmap]
rs12785559	0.80[EUR][1000 genomes]
rs12786377	0.80[EUR][1000 genomes]
rs12790020	0.80[EUR][1000 genomes]
rs12794962	0.84[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs12798311	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12805109	0.81[EUR][1000 genomes]
rs1347016	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985026	0.80[EUR][1000 genomes]
rs2016844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043218	0.80[EUR][1000 genomes]
rs2116510	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2116511	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163625	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2246878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252102	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2316541	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2568029	0.81[MEX][hapmap]
rs2568034	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2568042	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568047	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2568069	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568079	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2568086	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568087	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568088	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2653556	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2653562	0.84[EUR][1000 genomes]
rs2653565	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2653587	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2653590	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2653597	0.86[ASN][1000 genomes]
rs2653601	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];0.99[ASN][1000 genomes]
rs2653604	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2653611	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742486	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742487	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742488	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742489	0.85[ASN][1000 genomes]
rs2742491	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742496	0.91[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742497	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742502	0.86[MEX][hapmap]
rs2742504	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742505	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742513	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742514	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742519	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742520	0.83[EUR][1000 genomes]
rs2742521	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3751063	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs3751065	0.83[EUR][1000 genomes]
rs3751066	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs3751068	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs3763911	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs3763912	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4370967	0.84[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4909951	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4910181	0.91[EUR][1000 genomes]
rs4910313	0.80[EUR][1000 genomes]
rs7106152	0.81[EUR][1000 genomes]
rs7106539	0.82[EUR][1000 genomes]
rs7125458	0.81[MEX][hapmap]
rs72851596	0.92[ASN][1000 genomes]
rs72852790	0.92[ASN][1000 genomes]
rs72853712	0.92[ASN][1000 genomes]
rs7932377	0.81[EUR][1000 genomes]
rs7936201	0.81[MEX][hapmap]
rs7940895	0.85[ASN][1000 genomes]
rs7951226	0.81[EUR][1000 genomes]
rs909464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300096	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs982273	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2056903	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs2056903	OR52E6	cis	parietal	SCAN
rs2056903	C11orf17	cis	multi-tissue	Pritchard
rs2056903	MRVI1	cis	cerebellum	SCAN
rs2056903	TMEM9B	cis	multi-tissue	Pritchard
rs2056903	TMEM9B	cis	Liver	GTEx
rs2056903	C11orf17	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
4	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8934200-8941600	Weak transcription	Esophagus	oesophagus
6	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:8935000-8940400	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:8936400-8941800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
14	chr11:8936600-8940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:8936600-8940800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:8936600-8941400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:8936600-8941600	Weak transcription	Ovary	ovary
18	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
20	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
22	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
23	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:8936800-8942200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:8936800-8947000	Strong transcription	Dnd41	blood
26	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
29	chr11:8937200-8945000	Strong transcription	Brain Angular Gyrus	brain
30	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
31	chr11:8937600-8944800	Strong transcription	Hela-S3	cervix
32	chr11:8937800-8940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr11:8937800-8940800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:8938000-8940200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:8938000-8940200	Enhancers	Rectal Smooth Muscle	rectum
37	chr11:8938000-8941200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:8938000-8941200	Strong transcription	K562	blood
39	chr11:8938000-8943000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:8938000-8943200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr11:8938000-8944200	Strong transcription	HUVEC	blood vessel
42	chr11:8938000-8944600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr11:8938000-8944800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:8938000-8944800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:8938000-8944800	Strong transcription	Fetal Intestine Large	intestine
46	chr11:8938000-8945000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr11:8938000-8945000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:8938000-8945800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:8938000-8946400	Strong transcription	Brain Hippocampus Middle	brain
50	chr11:8938000-8946600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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