Variant report

Variant	rs675441
Chromosome Location	chr11:93505490-93505491
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93500100..93501816-chr11:93503980..93506998,3	K562	blood:
2	chr11:93475114..93477251-chr11:93501701..93505536,3	K562	blood:
3	chr11:93473228..93477931-chr11:93504576..93509493,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166012	Chromatin interaction
ENSG00000182919	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 25 )

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

rs_ID	r²[population]
rs10741476	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10765633	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10831102	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020505	0.96[CEU][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11020506	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020507	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020510	0.91[EUR][1000 genomes]
rs11020521	0.87[EUR][1000 genomes]
rs11020522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12292460	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1284102	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1284108	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1284141	0.85[AMR][1000 genomes]
rs1428919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783938	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2434984	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848477	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132750	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3132751	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4753103	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4753501	0.81[EUR][1000 genomes]
rs56364420	0.92[EUR][1000 genomes]
rs585713	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs586293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588644	0.86[EUR][1000 genomes]
rs595650	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598376	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598427	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs601711	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602242	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs602665	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs606087	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs606286	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs606357	0.91[EUR][1000 genomes]
rs606462	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs606749	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs607615	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs611762	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs616876	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs618801	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs621355	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs622147	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624856	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs625249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628661	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs630811	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs631177	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs631261	0.80[ASN][1000 genomes]
rs631705	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs640379	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs640382	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs640864	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644535	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs652621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652961	0.96[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs653939	0.92[EUR][1000 genomes]
rs655158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658181	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658698	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658797	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659877	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs662070	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs664619	0.84[AFR][1000 genomes]
rs665507	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs666136	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs670871	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs673869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675501	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676586	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs681321	0.92[EUR][1000 genomes]
rs687042	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs687507	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs688634	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693947	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7943266	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943525	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7950574	0.90[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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs675441	C11orf54	cis	lymphoblastoid	seeQTL
rs675441	SCARNA9	cis	parietal	SCAN
rs675441	C11orf54	cis	Thyroid	GTEx
rs675441	C11orf54	cis	Muscle Skeletal	GTEx
rs675441	C11orf54	cis	lung	GTEx
rs675441	GPR83	cis	cerebellum	SCAN
rs675441	MED17	cis	parietal	SCAN
rs675441	SNORA8	cis	cerebellum	SCAN
rs675441	C11orf54	cis	Heart Left Ventricle	GTEx
rs675441	ENDOD1	cis	cerebellum	SCAN
rs675441	C11orf54	cis	Esophagus Muscularis	GTEx
rs675441	SNORD5	cis	cerebellum	SCAN
rs675441	C11orf54	cis	Artery Tibial	GTEx
rs675441	C11orf54	cis	cerebellum	SCAN
rs675441	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs675441	MED17	cis	cerebellum	SCAN
rs675441	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs675441	C11orf54	cis	parietal	SCAN
rs675441	C11orf54	cis	Esophagus Mucosa	GTEx
rs675441	C11orf54	cis	Artery Aorta	GTEx
rs675441	C11orf54	cis	Stomach	GTEx
rs675441	C11orf54	cis	Nerve Tibial	GTEx
rs675441	C11orf54	cis	multi-tissue	Pritchard
rs675441	C11orf54	cis	Adipose Subcutaneous	GTEx
rs675441	FUT4	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:93492200-93506600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:93492200-93507400	Weak transcription	Aorta	Aorta
4	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
5	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
6	chr11:93493800-93507200	Weak transcription	Ovary	ovary
7	chr11:93494000-93506200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:93496000-93513600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:93497600-93506000	Weak transcription	Fetal Stomach	stomach
10	chr11:93498000-93516600	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:93498200-93505600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:93498600-93516600	Weak transcription	Hela-S3	cervix
13	chr11:93498800-93506000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:93499000-93505800	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:93499200-93505600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:93499200-93516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:93499600-93506400	Weak transcription	Primary T cells from cord blood	blood
18	chr11:93499800-93516600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:93503800-93505600	Weak transcription	HepG2	liver
20	chr11:93504200-93505600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:93504200-93506400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr11:93505000-93507400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:93505200-93506800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:93505200-93507000	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr11:93505400-93505600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:93505400-93505600	Strong transcription	Fetal Brain Female	brain
27	chr11:93505400-93505800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:93505400-93506400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:93505400-93506600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:93505400-93506800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:93505400-93506800	ZNF genes & repeats	Brain Germinal Matrix	brain

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