Variant report

Variant	rs11130329
Chromosome Location	chr3:52896855-52896856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10510761	0.87[GIH][hapmap]
rs1139106	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs11626	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs11705797	0.84[EUR][1000 genomes]
rs11707829	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708337	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11708390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710394	0.87[GIH][hapmap]
rs11712498	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713324	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713376	0.84[EUR][1000 genomes]
rs11713479	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714793	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715498	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11716506	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11716612	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11717619	0.87[GIH][hapmap]
rs11717749	1.00[CHB][hapmap]
rs11718060	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11720228	1.00[CHB][hapmap]
rs11720233	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720488	0.84[EUR][1000 genomes]
rs13060282	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062228	0.85[EUR][1000 genomes]
rs13067373	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13068194	0.85[EUR][1000 genomes]
rs13076033	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13080929	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs13089969	1.00[ASN][1000 genomes]
rs13095705	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	0.93[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2240916	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2336660	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2336661	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336662	1.00[YRI][hapmap]
rs2336665	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2710336	0.81[YRI][hapmap]
rs34026403	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230793	1.00[ASN][1000 genomes]
rs35404467	0.85[EUR][1000 genomes]
rs35569457	0.81[EUR][1000 genomes]
rs35651539	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126605	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3733034	1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs3733035	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs4608686	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687556	0.82[EUR][1000 genomes]
rs4687561	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4687676	0.84[EUR][1000 genomes]
rs4687681	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs56231111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61473083	0.84[EUR][1000 genomes]
rs6762260	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6773441	1.00[YRI][hapmap]
rs6798472	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299621	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	1.00[ASN][1000 genomes]
rs73839535	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9637477	0.84[EUR][1000 genomes]
rs9831977	1.00[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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11130329	TMEM110	cis	lymphoblastoid	seeQTL
rs11130329	TMEM110	cis	cerebellum	SCAN
rs11130329	TMEM110	cis	multi-tissue	Pritchard
rs11130329	GNAI2	cis	parietal	SCAN
rs11130329	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs11130329	DNAH1	cis	parietal	SCAN
rs11130329	DNAH1	cis	cerebellum	SCAN
rs11130329	ITIH4	cis	parietal	SCAN
rs11130329	MUSTN1	cis	cerebellum	SCAN
rs11130329	TMEM110	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:52886200-52907800	Weak transcription	NHLF	lung
6	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
8	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52886600-52899800	Weak transcription	Dnd41	blood
11	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
15	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
17	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
22	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:52887600-52898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
25	chr3:52888000-52898000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:52889000-52897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:52889200-52898200	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:52891400-52901600	Weak transcription	Right Atrium	heart
36	chr3:52891600-52909400	Weak transcription	Ovary	ovary
37	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
38	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
43	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:52894800-52897000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:52894800-52899800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:52895000-52898600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:52895200-52900400	Weak transcription	Lung	lung
50	chr3:52895400-52897000	Weak transcription	Primary monocytes fromperipheralblood	blood

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