Variant report

Variant	rs676586
Chromosome Location	chr11:93521405-93521406
allele	C/T
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	chr11:93472800..93476056-chr11:93515203..93522725,16	MCF-7	breast:
4	chr11:93477638..93479827-chr11:93520843..93522427,2	K562	blood:

Variant related genes	Relation type
ENSG00000202314	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000207145	Chromatin interaction
ENSG00000207112	Chromatin interaction
ENSG00000207304	Chromatin interaction
ENSG00000239195	Chromatin interaction
ENSG00000206834	Chromatin interaction
ENSG00000206799	Chromatin interaction
ENSG00000210825	Chromatin interaction
ENSG00000221170	Chromatin interaction
ENSG00000182919	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]
rs606087	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]
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];1.00[GIH][hapmap];0.85[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];0.96[GIH][hapmap];0.88[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]
rs67681709	0.86[EUR][1000 genomes]
rs677019	0.86[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs67734074	0.92[EUR][1000 genomes]
rs679241	0.86[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs687042	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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
rs676586	MED17	Cis_1M	lymphoblastoid	RTeQTL
rs676586	C11orf54	cis	parietal	SCAN

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	chr11:93519200-93522400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:93519200-93522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:93519200-93522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:93519200-93522800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:93519200-93522800	Weak transcription	Gastric	stomach
7	chr11:93519200-93522800	Weak transcription	HSMMtube	muscle
8	chr11:93519200-93523800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:93519200-93523800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:93519200-93527800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:93519200-93527800	Weak transcription	Esophagus	oesophagus
12	chr11:93519200-93542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:93519600-93522000	Weak transcription	A549	lung
14	chr11:93519800-93523800	Weak transcription	Fetal Stomach	stomach
15	chr11:93520000-93521600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:93520000-93521600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:93520000-93522400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:93520000-93523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:93520000-93523800	Weak transcription	Spleen	Spleen
20	chr11:93520000-93527000	Weak transcription	Colonic Mucosa	Colon
21	chr11:93520200-93521800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:93520200-93522000	Weak transcription	Brain Anterior Caudate	brain
23	chr11:93520200-93522000	Weak transcription	Fetal Kidney	kidney
24	chr11:93520200-93522000	Active TSS	GM12878-XiMat	blood
25	chr11:93520200-93522000	Weak transcription	NHLF	lung
26	chr11:93520200-93522200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:93520200-93522200	Weak transcription	Primary T cells from cord blood	blood
28	chr11:93520200-93522200	Weak transcription	HMEC	breast
29	chr11:93520200-93522400	Weak transcription	Ovary	ovary
30	chr11:93520200-93522600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr11:93520200-93522600	Weak transcription	Brain Substantia Nigra	brain
32	chr11:93520200-93522600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:93520200-93522800	Weak transcription	Aorta	Aorta
34	chr11:93520200-93549400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:93520200-93551000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:93520400-93521600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:93520400-93521600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:93520400-93521600	Weak transcription	Psoas Muscle	Psoas
39	chr11:93520400-93521800	Weak transcription	HepG2	liver
40	chr11:93520400-93522000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:93520400-93522400	Weak transcription	Left Ventricle	heart
42	chr11:93520400-93522600	Weak transcription	Thymus	Thymus
43	chr11:93520400-93522800	Weak transcription	Fetal Intestine Small	intestine
44	chr11:93520400-93522800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:93520400-93522800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:93520400-93523800	Weak transcription	Lung	lung
47	chr11:93520400-93523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:93520400-93524000	Weak transcription	Pancreas	Pancrea
49	chr11:93520400-93524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:93520400-93527800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links