Variant report

Variant	rs11626
Chromosome Location	chr3:52873984-52873985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10510761	0.87[GIH][hapmap]
rs11130329	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs1139106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707829	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11708390	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs11709430	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710394	0.87[GIH][hapmap]
rs11712498	1.00[CHB][hapmap]
rs11713324	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs11717619	0.87[GIH][hapmap]
rs11717749	1.00[CHB][hapmap]
rs11718060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720228	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11720233	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs13067373	0.81[CEU][hapmap]
rs13076033	1.00[CHB][hapmap]
rs13080929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	0.81[CEU][hapmap]
rs2001732	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071039	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2240916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276818	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276822	1.00[JPT][hapmap]
rs2336661	0.81[CEU][hapmap]
rs28552648	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999310	1.00[ASN][1000 genomes]
rs34288509	1.00[ASN][1000 genomes]
rs34860124	1.00[ASN][1000 genomes]
rs3755801	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755805	0.92[ASN][1000 genomes]
rs3796352	1.00[CHB][hapmap]
rs4687556	0.91[EUR][1000 genomes]
rs4687676	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798472	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs9637477	0.93[EUR][1000 genomes]
rs9831977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv967253	chr3:52871714-52877079	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11626	TMEM110	cis	Thyroid	GTEx
rs11626	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs11626	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:52865600-52875200	Weak transcription	Dnd41	blood
8	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
9	chr3:52866000-52884800	Weak transcription	HMEC	breast
10	chr3:52866200-52885200	Weak transcription	NHEK	skin
11	chr3:52866600-52879200	Weak transcription	Osteobl	bone
12	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
14	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
15	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
22	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
26	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
27	chr3:52869400-52874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:52869400-52875200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:52869400-52875600	Weak transcription	Colonic Mucosa	Colon
30	chr3:52869600-52875000	Strong transcription	Brain Angular Gyrus	brain
31	chr3:52869600-52875200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr3:52869600-52878600	Weak transcription	NHDF-Ad	bronchial
33	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:52869800-52874200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:52869800-52875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:52869800-52876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:52870000-52874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52870000-52874400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52870000-52875000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:52870000-52878800	Genic enhancers	Fetal Muscle Leg	muscle
44	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
45	chr3:52870200-52874000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:52870200-52874200	Weak transcription	Placenta	Placenta
47	chr3:52870200-52875600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:52870200-52876600	Strong transcription	Fetal Stomach	stomach
49	chr3:52870400-52875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:52870400-52876400	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links