Variant report

Variant	rs2336661
Chromosome Location	chr3:52900424-52900425
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52900079..52901582-chr3:52907440..52909357,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11130329	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]
rs1139106	0.81[CEU][hapmap]
rs11626	0.81[CEU][hapmap]
rs11705797	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11707829	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708337	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11708390	0.93[CEU][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712498	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11713324	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11713376	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11713479	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11714793	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715498	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716506	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716612	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11718060	0.81[CEU][hapmap]
rs11720233	0.93[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720488	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13060282	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13062228	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13067373	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13068194	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13076033	0.95[ASN][1000 genomes]
rs13080929	0.81[CEU][hapmap]
rs13089969	0.95[ASN][1000 genomes]
rs13095705	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1986656	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001732	0.93[CEU][hapmap]
rs2240916	0.81[CEU][hapmap]
rs2336660	1.00[YRI][hapmap]
rs2336662	1.00[YRI][hapmap]
rs2336665	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2710336	0.81[YRI][hapmap]
rs34026403	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35230793	0.95[ASN][1000 genomes]
rs35404467	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35569457	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35651539	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36126605	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733034	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733035	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3796352	0.95[ASN][1000 genomes]
rs4608686	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4687561	1.00[YRI][hapmap]
rs4687681	1.00[YRI][hapmap]
rs56231111	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61473083	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6762260	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6773441	1.00[YRI][hapmap]
rs6798472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71299621	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71299622	0.95[ASN][1000 genomes]
rs73839535	0.87[AMR][1000 genomes];0.99[EUR][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	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
rs2336661	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs2336661	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 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	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52886200-52907800	Weak transcription	NHLF	lung
4	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
8	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
10	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
12	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
14	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:52891400-52901600	Weak transcription	Right Atrium	heart
20	chr3:52891600-52909400	Weak transcription	Ovary	ovary
21	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
22	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
27	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:52895400-52904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:52895400-52907400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:52895600-52904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
36	chr3:52896200-52909800	Weak transcription	Gastric	stomach
37	chr3:52896400-52904400	Weak transcription	Right Ventricle	heart
38	chr3:52898400-52907400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:52898600-52904400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:52898800-52909600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:52899600-52900800	ZNF genes & repeats	Thymus	Thymus
42	chr3:52899800-52900600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr3:52899800-52900600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:52899800-52900600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52899800-52900800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:52899800-52900800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:52899800-52900800	Strong transcription	Aorta	Aorta
48	chr3:52899800-52901400	ZNF genes & repeats	Fetal Thymus	thymus
49	chr3:52900000-52900600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52900000-52900800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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