Variant report

Variant	rs652961
Chromosome Location	chr11:93476766-93476767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:93476104-93477124	HepG2	liver:	n/a	n/a
2	MAX	chr11:93476364-93476970	A549	lung:	n/a	n/a
3	POLR2A	chr11:93476530-93476772	K562	blood:	n/a	n/a
4	POLR2A	chr11:93476428-93476837	A549	lung:	n/a	n/a
5	POLR2A	chr11:93476511-93476866	A549	lung:	n/a	n/a
6	POLR2A	chr11:93476321-93477008	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr11:93476263-93477297	PANC-1	pancreas:	n/a	n/a
8	TCF7L2	chr11:93476574-93476777	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr11:93476725-93476787	A549	lung:	n/a	n/a
10	POLR2A	chr11:93476702-93477161	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:93476599-93477372	HepG2	liver:	n/a	n/a
12	MAX	chr11:93476378-93476888	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:93476721-93476771	HIPEpiC	eye:	n/a
2	chr11:93476721-93476771	GM12892	blood:	n/a
3	chr11:93476721-93476771	HRE	kidney:	n/a
4	chr11:93476721-93476771	BJ	skin:	n/a
5	chr11:93476721-93476771	HPAEpiC	pulmonary alveolar:	n/a
6	chr11:93476721-93476771	NB4	blood:	n/a
7	chr11:93476721-93476771	NH-A	brain:	n/a
8	chr11:93476721-93476771	SKMC	muscle:	n/a
9	chr11:93476721-93476771	NHBE	bronchial:	n/a
10	chr11:93476721-93476771	HNPCEpiC	eye:	n/a
11	chr11:93476721-93476771	HRCEpiC	kidney:	n/a
12	chr11:93476721-93476771	HCF	heart:	n/a
13	chr11:93476721-93476771	NT2-D1	testis:	n/a
14	chr11:93476721-93476771	Hepatocyte	liver:	n/a
15	chr11:93476721-93476771	LNCaP	prostate:	n/a
16	chr11:93476721-93476771	HCM	heart:	n/a
17	chr11:93476721-93476771	AG10803	skin:	n/a
18	chr11:93476721-93476771	PrEC	prostate:	n/a
19	chr11:93476721-93476771	HUVEC	blood vessel:	n/a
20	chr11:93476721-93476771	AG04449	skin:	fetal
21	chr11:93476721-93476771	GM19239	blood:	n/a
22	chr11:93476721-93476771	PANC-1	pancreas:	n/a
23	chr11:93476721-93476771	H1-hESC	embryonic stem cell:	embryo
24	chr11:93476721-93476771	MCF-7	breast:	n/a
25	chr11:93476721-93476771	AG09309	skin:	n/a
26	chr11:93476721-93476771	HAEpiC	amniotic membrane:	n/a
27	chr11:93476721-93476771	AG04450	lung:	fetal
28	chr11:93476721-93476771	A549	lung:	n/a
29	chr11:93476721-93476771	HL-60	blood:	n/a
30	chr11:93476721-93476771	Jurkat	blood:	n/a
31	chr11:93476721-93476771	NHDF-neo	bronchial:	n/a
32	chr11:93476721-93476771	SK-N-MC	brain:	n/a
33	chr11:93476721-93476771	T-47D	breast:	n/a
34	chr11:93476721-93476771	HCT-116	colon:	n/a
35	chr11:93476721-93476771	Caco-2	colon:	n/a
36	chr11:93476721-93476771	IMR90	lung:	fetal
37	chr11:93476721-93476771	ovcar-3	ovarian:	n/a
38	chr11:93476721-93476771	AoSMC	blood vessel:	n/a
39	chr11:93476721-93476771	SAEC	small airway:	n/a
40	chr11:93476721-93476771	ProgFib	skin:	n/a
41	chr11:93476721-93476771	SK-N-SH	brain:	n/a
42	chr11:93476721-93476771	HMEC	breast:	n/a
43	chr11:93476721-93476771	HEK293	kidney:	embryo
44	chr11:93476721-93476771	HRPEpiC	eye:	n/a
45	chr11:93476721-93476771	AG09319	gingival:	n/a
46	chr11:93476721-93476771	GM12878	blood:	n/a
47	chr11:93476721-93476771	RPTEC	kidney:	n/a
48	chr11:93476721-93476771	HEEpiC	esophagus:	n/a
49	chr11:93476721-93476771	K562	blood:	n/a
50	chr11:93476721-93476771	CMK	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:93475425..93477478-chr11:93478372..93480082,2	MCF-7	breast:
2	chr11:93475114..93477251-chr11:93501701..93505536,3	K562	blood:
3	chr11:93472589..93476859-chr11:93528988..93534877,8	K562	blood:
4	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:
5	chr11:93475019..93477218-chr11:93528354..93530806,2	K562	blood:
6	chr11:93475427..93477078-chr11:93480358..93482753,2	MCF-7	breast:
7	chr11:93476133..93478547-chr11:93497585..93500296,2	K562	blood:

No data

Variant related genes	Relation type
C11orf54	TF binding region
TAF1D	TF binding region
TAF1D	CpG island
C11orf54	CpG island
ENSG00000166012	Chromatin interaction
ENSG00000238437	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000265292	Chromatin interaction
ENSG00000042429	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 28 )

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

rs_ID	r²[population]
rs10741476	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10765633	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10765634	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10831102	0.91[EUR][1000 genomes]
rs11020505	1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020506	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11020507	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11020510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020521	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11020522	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs12292460	0.89[EUR][1000 genomes]
rs1284102	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1284108	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1284141	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1428919	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1783938	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2434984	0.89[EUR][1000 genomes]
rs2848477	0.90[EUR][1000 genomes]
rs3132750	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132751	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4753103	0.90[EUR][1000 genomes]
rs56364420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585713	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs586293	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs588644	0.85[EUR][1000 genomes]
rs59031514	0.81[ASN][1000 genomes]
rs595650	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs598376	0.91[EUR][1000 genomes]
rs598427	0.86[EUR][1000 genomes]
rs602242	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs602665	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs606286	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs606357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606462	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs606749	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs607615	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs611762	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs616876	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs618801	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621355	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs622147	0.92[EUR][1000 genomes]
rs624856	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs625249	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs628661	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs630811	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs631177	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs631705	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs640379	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs640382	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs640864	0.91[EUR][1000 genomes]
rs644009	0.96[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs644535	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs652621	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs653939	0.97[EUR][1000 genomes]
rs655158	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs655699	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs658181	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs658698	0.87[EUR][1000 genomes]
rs658797	0.92[EUR][1000 genomes]
rs659877	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs662070	0.84[EUR][1000 genomes]
rs66460850	0.81[ASN][1000 genomes]
rs665507	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs666136	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs670871	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs673869	0.96[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs675441	0.96[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs675501	0.92[EUR][1000 genomes]
rs681321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688634	0.93[EUR][1000 genomes]
rs693947	0.90[EUR][1000 genomes]
rs7131178	0.81[JPT][hapmap]
rs7943266	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7943525	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7950574	0.83[AMR][1000 genomes];0.95[EUR][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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs652961	FUT4	cis	cerebellum	SCAN
rs652961	ENDOD1	cis	cerebellum	SCAN
rs652961	C11orf54	cis	parietal	SCAN
rs652961	GPR83	cis	cerebellum	SCAN
rs652961	C11orf54	cis	Nerve Tibial	GTEx
rs652961	C11orf54	cis	normal skin	skin_eQTL
rs652961	C11orf54	cis	cerebellum	SCAN
rs652961	C11orf54	cis	lung	GTEx
rs652961	MED17	cis	cerebellum	SCAN
rs652961	C11orf54	cis	Stomach	GTEx
rs652961	PTD012	cis	multi-tissue	Pritchard
rs652961	C11orf54	cis	Whole Blood	GTEx
rs652961	C11orf54	cis	uninvolved skin	skin_eQTL
rs652961	C11orf54	cis	multi-tissue	Pritchard
rs652961	C11orf54	cis	Artery Aorta	GTEx
rs652961	C11orf54	cis	Adipose Subcutaneous	GTEx
rs652961	C11orf54	cis	Heart Left Ventricle	GTEx
rs652961	C11orf54	cis	lesional skin	skin_eQTL
rs652961	MED17	cis	parietal	SCAN
rs652961	C11orf54	cis	lymphoblastoid	seeQTL
rs652961	SCARNA9	cis	parietal	SCAN
rs652961	C11orf54	cis	Esophagus Mucosa	GTEx
rs652961	C11orf54	cis	Esophagus Muscularis	GTEx
rs652961	C11orf54	cis	Artery Tibial	GTEx
rs652961	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs652961	C11orf54	cis	Thyroid	GTEx
rs652961	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs652961	C11orf54	cis	Muscle Skeletal	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	chr11:93475600-93477000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr11:93475600-93478000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:93475600-93478000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:93475600-93490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:93475600-93497000	Weak transcription	NHDF-Ad	bronchial
12	chr11:93475800-93476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:93475800-93477200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:93475800-93478200	Enhancers	Fetal Heart	heart
15	chr11:93475800-93488400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:93475800-93488400	Weak transcription	Aorta	Aorta
17	chr11:93476000-93476800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:93476000-93476800	Enhancers	Small Intestine	intestine
19	chr11:93476000-93476800	Weak transcription	HSMM	muscle
20	chr11:93476000-93477000	Weak transcription	Brain Hippocampus Middle	brain
21	chr11:93476000-93477200	Genic enhancers	Fetal Intestine Small	intestine
22	chr11:93476000-93477200	Genic enhancers	Fetal Muscle Leg	muscle
23	chr11:93476000-93477400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:93476000-93477800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:93476000-93477800	Weak transcription	Psoas Muscle	Psoas
26	chr11:93476000-93478000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:93476000-93478000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:93476000-93478000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:93476000-93478000	Weak transcription	Adipose Nuclei	Adipose
30	chr11:93476000-93478000	Weak transcription	Brain Anterior Caudate	brain
31	chr11:93476000-93478000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:93476000-93478200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:93476000-93478200	Weak transcription	Brain Substantia Nigra	brain
34	chr11:93476000-93481800	Weak transcription	Thymus	Thymus
35	chr11:93476000-93483000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:93476000-93486600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:93476000-93486800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr11:93476000-93488400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:93476000-93488400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:93476000-93488400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr11:93476000-93488400	Weak transcription	HSMMtube	muscle
42	chr11:93476000-93490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:93476000-93491400	Weak transcription	Osteobl	bone
44	chr11:93476000-93495600	Weak transcription	HUVEC	blood vessel
45	chr11:93476000-93497000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:93476000-93497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:93476200-93476800	Weak transcription	Fetal Kidney	kidney
49	chr11:93476200-93476800	Weak transcription	K562	blood
50	chr11:93476200-93477000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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