Variant report

Variant	rs13062228
Chromosome Location	chr3:52932744-52932745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52932381-52932756	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:52932297-52932761	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52932221..52934839-chr3:53107486..53109426,2	K562	blood:

Variant related genes	Relation type
TMEM110-MUSTN1	TF binding region
TMEM110	TF binding region

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

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10510761	0.89[ASN][1000 genomes]
rs11130329	0.85[EUR][1000 genomes]
rs11705797	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706035	0.82[ASN][1000 genomes]
rs11707829	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708337	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708390	0.86[EUR][1000 genomes]
rs11710394	0.82[ASN][1000 genomes]
rs11710707	0.89[ASN][1000 genomes]
rs11712498	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713206	0.82[ASN][1000 genomes]
rs11713290	0.83[ASN][1000 genomes]
rs11713324	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713376	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713479	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714037	0.89[ASN][1000 genomes]
rs11714793	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11715231	1.00[ASN][1000 genomes]
rs11715498	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716506	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716612	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717132	0.89[ASN][1000 genomes]
rs11717619	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11717715	0.89[ASN][1000 genomes]
rs11718538	0.89[ASN][1000 genomes]
rs11718834	0.89[ASN][1000 genomes]
rs11720191	0.82[ASN][1000 genomes]
rs11720233	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11720488	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060282	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13067373	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068194	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069006	0.89[ASN][1000 genomes]
rs13072395	0.89[ASN][1000 genomes]
rs13074524	0.89[ASN][1000 genomes]
rs13078834	0.83[ASN][1000 genomes]
rs13091844	0.82[ASN][1000 genomes]
rs13092352	0.89[ASN][1000 genomes]
rs13095705	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986656	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336540	0.89[ASN][1000 genomes]
rs2336541	0.89[ASN][1000 genomes]
rs2336661	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336665	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34026403	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34313969	0.82[ASN][1000 genomes]
rs34493168	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	0.82[ASN][1000 genomes]
rs35385050	0.82[ASN][1000 genomes]
rs35404467	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35569457	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35651539	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35720014	0.89[ASN][1000 genomes]
rs35737577	0.82[ASN][1000 genomes]
rs35849389	0.82[ASN][1000 genomes]
rs36090694	0.82[ASN][1000 genomes]
rs36126605	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733034	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733035	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4608686	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56231111	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58515094	0.82[ASN][1000 genomes]
rs60887045	0.89[ASN][1000 genomes]
rs60942590	0.82[ASN][1000 genomes]
rs61172708	0.82[ASN][1000 genomes]
rs61473083	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762260	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798472	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71299621	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71299700	0.82[ASN][1000 genomes]
rs73839535	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
3	esv3339338	chr3:52930462-52933260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13062228	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs13062228	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931600-52945000	Weak transcription	Gastric	stomach
2	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
3	chr3:52932000-52935200	Weak transcription	Right Atrium	heart
4	chr3:52932000-52936200	Weak transcription	Fetal Intestine Large	intestine
5	chr3:52932000-52937000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:52932000-52938200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:52932000-52938600	Weak transcription	Left Ventricle	heart
8	chr3:52932000-52938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:52932000-52939000	Weak transcription	Aorta	Aorta
10	chr3:52932000-52939000	Weak transcription	Psoas Muscle	Psoas
11	chr3:52932000-52940000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:52932000-52941000	Weak transcription	Lung	lung
13	chr3:52932000-52943600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:52932000-52943800	Weak transcription	Pancreas	Pancrea
15	chr3:52932000-52946400	Weak transcription	Esophagus	oesophagus
16	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
18	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:52932200-52934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:52932200-52935800	Weak transcription	Fetal Brain Female	brain
23	chr3:52932200-52936000	Weak transcription	Primary T cells from cord blood	blood
24	chr3:52932200-52936200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:52932200-52936200	Weak transcription	Liver	Liver
26	chr3:52932200-52936200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52932200-52936800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:52932200-52937200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:52932200-52937400	Weak transcription	Primary B cells from cord blood	blood
30	chr3:52932200-52937600	Weak transcription	HepG2	liver
31	chr3:52932200-52937600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:52932200-52937800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:52932200-52937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:52932200-52937800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52932200-52937800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:52932200-52937800	Weak transcription	Placenta	Placenta
37	chr3:52932200-52938000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:52932200-52938000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:52932200-52938000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:52932200-52938000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:52932200-52938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:52932200-52938000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:52932200-52938200	Weak transcription	Fetal Intestine Small	intestine
44	chr3:52932200-52938800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:52932200-52939000	Weak transcription	GM12878-XiMat	blood
46	chr3:52932200-52939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:52932200-52940000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:52932200-52940200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:52932200-52940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:52932200-52940800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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