Variant report

Variant	rs10741476
Chromosome Location	chr11:93477621-93477622
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	POLR2A	chr11:93477592-93477775	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:93476771-93478601	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93476858..93478518-chr11:93487193..93489056,2	K562	blood:
2	chr11:93476133..93478547-chr11:93497585..93500296,2	K562	blood:

Variant related genes	Relation type
C11orf54	TF binding region
TAF1D	TF binding region
ENSG00000182919	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10765633	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10765634	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10831102	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020506	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][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]
rs11020507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11020510	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020521	0.86[EUR][1000 genomes]
rs11020522	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12292460	0.89[EUR][1000 genomes]
rs12803773	0.87[AFR][1000 genomes]
rs1284102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1284108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1284141	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1428919	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1783938	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434978	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2434984	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2510603	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2848477	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3132750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132751	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4753103	0.90[EUR][1000 genomes]
rs56364420	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs585713	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs586293	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs588644	0.86[EUR][1000 genomes]
rs595650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598376	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598427	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs602242	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs606286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606357	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs606462	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606749	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607615	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs611762	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616876	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618801	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622147	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs624856	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625249	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs628661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631177	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631705	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640379	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640382	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640864	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs644009	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs644535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483265	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs652621	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs652961	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs653939	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655158	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs655699	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs658181	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs658698	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs658797	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs659877	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662070	0.84[EUR][1000 genomes]
rs665507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673869	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs675441	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs675501	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs681321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs688634	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs693947	0.90[EUR][1000 genomes]
rs7943266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7943525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950574	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs10741476	C11orf54	cis	Stomach	GTEx
rs10741476	C11orf54	cis	Nerve Tibial	GTEx
rs10741476	C11orf54	cis	uninvolved skin	skin_eQTL
rs10741476	C11orf54	cis	Esophagus Muscularis	GTEx
rs10741476	C11orf54	cis	lesional skin	skin_eQTL
rs10741476	C11orf54	cis	Heart Left Ventricle	GTEx
rs10741476	C11orf54	cis	Artery Aorta	GTEx
rs10741476	C11orf54	cis	normal skin	skin_eQTL
rs10741476	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs10741476	C11orf54	cis	Artery Tibial	GTEx
rs10741476	C11orf54	cis	Esophagus Mucosa	GTEx
rs10741476	C11orf54	cis	Adipose Subcutaneous	GTEx
rs10741476	C11orf54	cis	Thyroid	GTEx
rs10741476	C11orf54	cis	multi-tissue	Pritchard
rs10741476	C11orf54	cis	lung	GTEx
rs10741476	C11orf54	cis	Muscle Skeletal	GTEx
rs10741476	C11orf54	cis	Whole Blood	GTEx
rs10741476	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93475200-93497000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:93475400-93478000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:93475400-93478200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:93475400-93478600	Enhancers	Stomach Mucosa	stomach
5	chr11:93475400-93490800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:93475400-93490800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:93475600-93478000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:93475600-93478000	Weak transcription	Brain Angular Gyrus	brain
9	chr11:93475600-93490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:93475600-93497000	Weak transcription	NHDF-Ad	bronchial
11	chr11:93475800-93478200	Enhancers	Fetal Heart	heart
12	chr11:93475800-93488400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:93475800-93488400	Weak transcription	Aorta	Aorta
14	chr11:93476000-93477800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:93476000-93477800	Weak transcription	Psoas Muscle	Psoas
16	chr11:93476000-93478000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:93476000-93478000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:93476000-93478000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:93476000-93478000	Weak transcription	Adipose Nuclei	Adipose
20	chr11:93476000-93478000	Weak transcription	Brain Anterior Caudate	brain
21	chr11:93476000-93478000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:93476000-93478200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:93476000-93478200	Weak transcription	Brain Substantia Nigra	brain
24	chr11:93476000-93481800	Weak transcription	Thymus	Thymus
25	chr11:93476000-93483000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:93476000-93486600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:93476000-93486800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:93476000-93488400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:93476000-93488400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:93476000-93488400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:93476000-93488400	Weak transcription	HSMMtube	muscle
32	chr11:93476000-93490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:93476000-93491400	Weak transcription	Osteobl	bone
34	chr11:93476000-93495600	Weak transcription	HUVEC	blood vessel
35	chr11:93476000-93497000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:93476000-93497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:93476200-93478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:93476200-93478400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:93476200-93482400	Weak transcription	Primary T cells from cord blood	blood
41	chr11:93476200-93483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:93476200-93486800	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:93476200-93488000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:93476200-93499800	Weak transcription	NH-A	brain
45	chr11:93476400-93477800	Enhancers	Stomach Smooth Muscle	stomach
46	chr11:93476400-93481800	Weak transcription	Primary B cells from cord blood	blood
47	chr11:93476600-93477800	Weak transcription	Brain Germinal Matrix	brain
48	chr11:93476600-93478600	Enhancers	Right Atrium	heart
49	chr11:93476600-93486400	Weak transcription	GM12878-XiMat	blood
50	chr11:93476600-93487200	Weak transcription	Fetal Brain Male	brain

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