Variant report

Variant	rs11712498
Chromosome Location	chr3:52905376-52905377
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	chr3:52903853..52907646-chr3:52911407..52913570,4	K562	blood:
2	chr3:52903586..52906484-chr3:52914418..52917233,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11130329	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139106	1.00[CHB][hapmap]
rs11626	1.00[CHB][hapmap]
rs11705797	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11707829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708337	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11708390	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713376	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11713479	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714793	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715498	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716506	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716612	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11717749	1.00[CHB][hapmap]
rs11718060	1.00[CHB][hapmap]
rs11720228	1.00[CHB][hapmap]
rs11720233	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720488	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13060282	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062228	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13067373	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13068194	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13076033	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13089969	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13095705	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001732	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2240916	1.00[CHB][hapmap]
rs2336661	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336665	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34026403	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230793	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35404467	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35569457	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35651539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126605	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733034	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733035	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774362	1.00[YRI][hapmap]
rs3796352	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4608686	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56231111	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61473083	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6762260	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299621	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73839535	0.88[AMR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712498	TMEM110	cis	multi-tissue	Pritchard
rs11712498	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52886200-52907800	Weak transcription	NHLF	lung
3	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
9	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
11	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:52891600-52909400	Weak transcription	Ovary	ovary
18	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
19	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:52895400-52907400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
29	chr3:52896200-52909800	Weak transcription	Gastric	stomach
30	chr3:52898400-52907400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:52898800-52909600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:52900000-52912800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:52900200-52905800	Weak transcription	Dnd41	blood
34	chr3:52900600-52907200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:52900600-52909000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52900600-52912200	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:52900800-52907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:52900800-52907600	Weak transcription	Aorta	Aorta
39	chr3:52900800-52909400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:52900800-52912400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:52900800-52912800	Weak transcription	Fetal Intestine Small	intestine
42	chr3:52900800-52913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:52901400-52908200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:52901400-52910200	Weak transcription	Spleen	Spleen
45	chr3:52901800-52912800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:52902000-52907600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr3:52902000-52907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52902000-52909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:52902200-52908400	Weak transcription	GM12878-XiMat	blood
50	chr3:52902200-52925200	Weak transcription	Placenta	Placenta

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