Variant report

Variant	rs658797
Chromosome Location	chr11:93519737-93519738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:93519571-93519779	K562	blood:	n/a	n/a
2	POLR2A	chr11:93519648-93519769	H1-hESC	embryonic stem cell:	n/a	n/a
3	WRNIP1	chr11:93519717-93519877	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:
2	chr11:93468648..93476533-chr11:93513626..93520226,41	K562	blood:
3	chr11:93468490..93476714-chr11:93515963..93520210,25	MCF-7	breast:
4	chr11:93472800..93476056-chr11:93515203..93522725,16	MCF-7	breast:
5	chr11:93459100..93466497-chr11:93514555..93520746,14	K562	blood:

No data

Variant related genes	Relation type
TAF1D	TF binding region
MED17	TF binding region
ENSG00000182919	Chromatin interaction
ENSG00000207112	Chromatin interaction
ENSG00000207145	Chromatin interaction
ENSG00000206799	Chromatin interaction
ENSG00000206834	Chromatin interaction
ENSG00000207304	Chromatin interaction
ENSG00000239195	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000210825	Chromatin interaction
ENSG00000221170	Chromatin interaction
ENSG00000202314	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10741476	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10765633	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10765634	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10831102	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020505	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11020506	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020510	0.91[EUR][1000 genomes]
rs11020521	0.94[EUR][1000 genomes]
rs11020522	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12292460	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1284102	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1284108	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1284141	0.90[AMR][1000 genomes]
rs1428919	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783938	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2434984	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510603	0.82[AMR][1000 genomes]
rs2848477	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132750	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132751	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4753103	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4753501	0.91[AFR][1000 genomes]
rs56364420	0.93[EUR][1000 genomes]
rs585713	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs586293	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588644	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs595650	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598376	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598427	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs601711	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602242	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs602665	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs606087	0.87[ASN][1000 genomes]
rs606286	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs606357	0.92[EUR][1000 genomes]
rs606462	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs606749	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs607615	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs611762	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs616876	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs618801	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs621355	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs622147	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624856	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs625249	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628661	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs630811	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631177	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631261	0.80[ASN][1000 genomes]
rs631705	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs640379	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs640382	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs640864	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644009	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644535	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs652621	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652961	0.92[EUR][1000 genomes]
rs653939	0.93[EUR][1000 genomes]
rs655158	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655699	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658181	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658698	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs659877	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs662070	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs665507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs666136	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs670871	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs673869	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675441	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675501	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676586	0.87[ASN][1000 genomes]
rs681321	0.92[EUR][1000 genomes]
rs687042	0.81[ASN][1000 genomes]
rs688634	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693947	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7943266	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943525	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7950574	0.85[AMR][1000 genomes];0.92[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs658797	C11orf54	cis	Esophagus Mucosa	GTEx
rs658797	C11orf54	cis	Artery Aorta	GTEx
rs658797	C11orf54	cis	Esophagus Muscularis	GTEx
rs658797	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs658797	C11orf54	cis	Nerve Tibial	GTEx
rs658797	C11orf54	cis	Adipose Subcutaneous	GTEx
rs658797	C11orf54	cis	lung	GTEx
rs658797	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs658797	C11orf54	cis	Heart Left Ventricle	GTEx
rs658797	C11orf54	cis	Muscle Skeletal	GTEx
rs658797	C11orf54	cis	Artery Tibial	GTEx
rs658797	C11orf54	cis	Stomach	GTEx
rs658797	C11orf54	cis	multi-tissue	Pritchard
rs658797	C11orf54	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93516800-93519800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:93516800-93520400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:93517600-93520800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr11:93517800-93520400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr11:93518000-93520200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:93518200-93520000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr11:93518200-93520000	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr11:93518200-93520400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:93518400-93519800	Active TSS	HepG2	liver
10	chr11:93518400-93520200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr11:93518600-93520000	Enhancers	Placenta	Placenta
12	chr11:93518600-93520200	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr11:93518600-93520200	Flanking Active TSS	HUVEC	blood vessel
14	chr11:93518600-93520400	Enhancers	Pancreas	Pancrea
15	chr11:93518600-93520400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
16	chr11:93518600-93520600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:93518600-93520800	Enhancers	Small Intestine	intestine
18	chr11:93518600-93527800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:93518800-93519800	Flanking Active TSS	NH-A	brain
20	chr11:93518800-93520000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:93518800-93520000	Flanking Active TSS	NHEK	skin
22	chr11:93518800-93520200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:93518800-93520200	Flanking Active TSS	Fetal Brain Female	brain
24	chr11:93518800-93520400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:93518800-93520800	Transcr. at gene 5' and 3'	Hela-S3	cervix
26	chr11:93518800-93521400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:93519000-93519800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr11:93519000-93520000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:93519000-93520000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr11:93519000-93520000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr11:93519000-93520200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:93519000-93520200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
33	chr11:93519000-93520200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
34	chr11:93519000-93520200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr11:93519000-93520200	Enhancers	Brain Substantia Nigra	brain
36	chr11:93519000-93520400	Enhancers	Primary B cells from peripheral blood	blood
37	chr11:93519000-93520400	Enhancers	Adipose Nuclei	Adipose
38	chr11:93519000-93520400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr11:93519000-93520400	Genic enhancers	Fetal Intestine Small	intestine
40	chr11:93519000-93520400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr11:93519000-93520600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr11:93519000-93520800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:93519000-93520800	Enhancers	Fetal Heart	heart
44	chr11:93519000-93521400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:93519200-93519800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr11:93519200-93519800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:93519200-93519800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:93519200-93519800	Enhancers	Brain Angular Gyrus	brain
49	chr11:93519200-93519800	Enhancers	Fetal Stomach	stomach
50	chr11:93519200-93520000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links