Variant report

Variant	rs606087
Chromosome Location	chr11:93522642-93522643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:
2	chr11:93473309..93475727-chr11:93520593..93523450,3	MCF-7	breast:
3	chr11:93469868..93471439-chr11:93522449..93523956,2	K562	blood:
4	chr11:93472800..93476056-chr11:93515203..93522725,16	MCF-7	breast:
5	chr11:93472896..93475000-chr11:93521473..93523956,3	K562	blood:

Variant related genes	Relation type
ENSG00000239195	Chromatin interaction
ENSG00000210825	Chromatin interaction
ENSG00000207145	Chromatin interaction
ENSG00000202314	Chromatin interaction
ENSG00000221170	Chromatin interaction
ENSG00000207112	Chromatin interaction
ENSG00000206799	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000207304	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000206834	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10831102	0.87[ASN][1000 genomes]
rs11020522	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1150326	0.96[EUR][1000 genomes]
rs1298531	0.82[CEU][hapmap]
rs1428919	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2077408	0.83[EUR][1000 genomes]
rs2848477	0.87[ASN][1000 genomes]
rs34057693	0.95[EUR][1000 genomes]
rs3763808	0.92[EUR][1000 genomes]
rs4753103	0.87[ASN][1000 genomes]
rs55734929	0.90[EUR][1000 genomes]
rs585713	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs586293	0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs598376	0.87[ASN][1000 genomes]
rs598495	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs602703	0.86[ASN][1000 genomes]
rs61498836	0.88[EUR][1000 genomes]
rs615428	0.93[EUR][1000 genomes]
rs61904953	0.95[EUR][1000 genomes]
rs61904957	0.92[EUR][1000 genomes]
rs622147	0.87[ASN][1000 genomes]
rs625249	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs625359	0.86[ASN][1000 genomes]
rs628665	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs631261	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs634325	0.83[ASN][1000 genomes]
rs640864	0.87[ASN][1000 genomes]
rs644009	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs652621	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs654896	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs655158	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs655699	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs658181	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs658698	0.81[ASN][1000 genomes]
rs658797	0.87[ASN][1000 genomes]
rs664257	0.92[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs66460850	0.83[EUR][1000 genomes]
rs66483735	0.86[EUR][1000 genomes]
rs66487029	0.95[EUR][1000 genomes]
rs666074	0.85[ASN][1000 genomes]
rs66760087	0.95[EUR][1000 genomes]
rs66797025	0.86[EUR][1000 genomes]
rs669565	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs670391	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs673869	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs674886	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs675441	0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs675501	0.87[ASN][1000 genomes]
rs67594435	0.95[EUR][1000 genomes]
rs676586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[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];1.00[ASN][1000 genomes]
rs67681709	0.86[EUR][1000 genomes]
rs677019	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes]
rs67734074	0.92[EUR][1000 genomes]
rs679241	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs687042	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs687507	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs688634	0.87[ASN][1000 genomes]
rs72976543	0.86[EUR][1000 genomes]
rs72976568	0.86[EUR][1000 genomes]
rs7814	0.85[CEU][hapmap]
rs7949505	0.94[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs606087	C11orf54	cis	parietal	SCAN
rs606087	MED17	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93518600-93527800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:93519200-93522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:93519200-93522800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:93519200-93522800	Weak transcription	Gastric	stomach
5	chr11:93519200-93522800	Weak transcription	HSMMtube	muscle
6	chr11:93519200-93523800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:93519200-93523800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:93519200-93527800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:93519200-93527800	Weak transcription	Esophagus	oesophagus
10	chr11:93519200-93542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:93519800-93523800	Weak transcription	Fetal Stomach	stomach
12	chr11:93520000-93523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:93520000-93523800	Weak transcription	Spleen	Spleen
14	chr11:93520000-93527000	Weak transcription	Colonic Mucosa	Colon
15	chr11:93520200-93522800	Weak transcription	Aorta	Aorta
16	chr11:93520200-93549400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:93520200-93551000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:93520400-93522800	Weak transcription	Fetal Intestine Small	intestine
19	chr11:93520400-93522800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:93520400-93522800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:93520400-93523800	Weak transcription	Lung	lung
22	chr11:93520400-93523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:93520400-93524000	Weak transcription	Pancreas	Pancrea
24	chr11:93520400-93524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:93520400-93527800	Weak transcription	Right Ventricle	heart
26	chr11:93520400-93529600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:93520400-93529600	Weak transcription	Stomach Mucosa	stomach
28	chr11:93520400-93549200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:93520400-93549400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:93520600-93524000	Weak transcription	Brain Germinal Matrix	brain
31	chr11:93520600-93540000	Weak transcription	Right Atrium	heart
32	chr11:93520600-93548200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:93520600-93551000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:93520800-93523000	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:93520800-93523000	Genic enhancers	Dnd41	blood
36	chr11:93520800-93523400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:93520800-93523400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:93520800-93523600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:93520800-93523800	Weak transcription	Small Intestine	intestine
40	chr11:93520800-93527000	Weak transcription	Fetal Heart	heart
41	chr11:93520800-93529400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:93520800-93549000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:93520800-93549200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:93520800-93549200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:93520800-93549400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:93520800-93549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:93520800-93549400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:93521000-93522800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:93521000-93523000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:93521000-93525000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links