Variant report

Variant	rs13095705
Chromosome Location	chr3:52958304-52958305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10510761	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11130329	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11705797	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706035	0.81[CEU][hapmap];0.82[ASN][1000 genomes]
rs11707829	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11708337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708390	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11710394	1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11710707	0.89[ASN][1000 genomes]
rs11712498	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11713206	0.82[ASN][1000 genomes]
rs11713290	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11713324	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11713376	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713479	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11714037	0.89[ASN][1000 genomes]
rs11714793	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715231	1.00[ASN][1000 genomes]
rs11715498	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716506	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717132	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11717619	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11717715	0.89[ASN][1000 genomes]
rs11718538	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11718834	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11720191	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11720233	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11720488	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060282	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13062228	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067373	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068194	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069006	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs13072395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13074524	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13078834	0.83[ASN][1000 genomes]
rs13091844	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs13092352	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1986656	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2001732	0.85[CEU][hapmap]
rs2336540	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2336541	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2336661	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2336665	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34026403	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34313969	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34493168	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34872575	0.89[ASN][1000 genomes]
rs34933390	0.82[ASN][1000 genomes]
rs34943350	0.82[ASN][1000 genomes]
rs35378159	0.89[ASN][1000 genomes]
rs35384050	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35385050	0.82[ASN][1000 genomes]
rs35404467	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35569457	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35651539	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35720014	0.89[ASN][1000 genomes]
rs35737577	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35849389	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs36090694	0.82[ASN][1000 genomes]
rs36126605	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733034	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4608686	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56231111	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58515094	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs60887045	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs60942590	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61172708	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61473083	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762260	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798472	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71299621	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71299700	0.82[ASN][1000 genomes]
rs73839535	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13095705	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs13095705	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
6	chr3:52932200-52961800	Weak transcription	A549	lung
7	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
8	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52932200-52967800	Weak transcription	HSMM	muscle
10	chr3:52932200-52968600	Weak transcription	Osteobl	bone
11	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
13	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
15	chr3:52932400-52968800	Weak transcription	NHEK	skin
16	chr3:52935600-52968600	Strong transcription	Dnd41	blood
17	chr3:52937200-52959800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:52938000-52959000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:52939600-52961200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:52941800-52961600	Weak transcription	Colonic Mucosa	Colon
21	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
22	chr3:52943200-52958800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:52943200-52958800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:52943600-52962400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:52943600-52964000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:52945200-52960000	Weak transcription	Gastric	stomach
27	chr3:52947400-52968000	Weak transcription	Fetal Lung	lung
28	chr3:52947600-52960800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:52947600-52963000	Weak transcription	Fetal Heart	heart
30	chr3:52949000-52962400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:52949000-52968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:52949200-52962800	Weak transcription	K562	blood
33	chr3:52950000-52966600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:52951200-52958800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:52951200-52959000	Strong transcription	Liver	Liver
36	chr3:52951200-52966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:52951400-52964400	Strong transcription	Fetal Intestine Large	intestine
38	chr3:52951600-52959200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:52952000-52968600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:52952600-52958400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:52952800-52965600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:52953000-52963000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:52953400-52958800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:52953400-52961400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:52953400-52961400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr3:52953800-52964600	Weak transcription	Fetal Kidney	kidney
47	chr3:52954000-52960000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:52954000-52962000	Weak transcription	HMEC	breast
49	chr3:52954000-52964000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus

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