Variant report

Variant	rs2336666
Chromosome Location	chr3:52915712-52915713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52915631..52918262-chr3:52921069..52922995,2	MCF-7	breast:
2	chr3:52903586..52906484-chr3:52914418..52917233,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11130332	0.85[EUR][1000 genomes]
rs1134546	0.91[EUR][1000 genomes]
rs11707576	0.83[EUR][1000 genomes]
rs11708223	0.84[EUR][1000 genomes]
rs12487379	0.83[ASN][1000 genomes]
rs12492391	0.86[ASN][1000 genomes]
rs12496077	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12638968	0.86[ASN][1000 genomes]
rs13082061	0.85[EUR][1000 genomes]
rs13083728	0.84[ASN][1000 genomes]
rs1573815	0.84[ASN][1000 genomes]
rs2276825	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2336162	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2336667	0.81[ASN][1000 genomes]
rs2336668	0.80[ASN][1000 genomes]
rs2336669	0.83[EUR][1000 genomes]
rs2336671	0.80[EUR][1000 genomes]
rs2581797	0.85[EUR][1000 genomes]
rs2581801	0.85[EUR][1000 genomes]
rs2581802	0.85[EUR][1000 genomes]
rs2581805	0.84[EUR][1000 genomes]
rs2581810	0.88[EUR][1000 genomes]
rs2581815	0.85[EUR][1000 genomes]
rs2581820	0.82[EUR][1000 genomes]
rs2581823	0.81[EUR][1000 genomes]
rs2710342	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710345	0.85[EUR][1000 genomes]
rs2878762	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35380116	0.82[EUR][1000 genomes]
rs3733047	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3821873	0.81[ASN][1000 genomes]
rs4302374	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4519686	0.83[EUR][1000 genomes]
rs4687559	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687560	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687562	0.84[ASN][1000 genomes]
rs4687663	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4687672	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4687680	0.85[ASN][1000 genomes]
rs4687682	0.81[ASN][1000 genomes]
rs4687683	0.80[ASN][1000 genomes]
rs6445538	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6445539	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6445547	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445550	0.85[EUR][1000 genomes]
rs6768844	0.83[EUR][1000 genomes]
rs6770957	0.84[EUR][1000 genomes]
rs6771610	0.83[EUR][1000 genomes]
rs6773040	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6792578	0.83[EUR][1000 genomes]
rs6795646	0.86[ASN][1000 genomes]
rs6797399	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798941	0.87[ASN][1000 genomes]
rs7620706	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7621939	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7638524	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7648514	0.83[EUR][1000 genomes]
rs7652131	0.84[EUR][1000 genomes]
rs9311485	0.83[EUR][1000 genomes]
rs9682464	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812543	0.84[EUR][1000 genomes]
rs9825230	0.84[ASN][1000 genomes]
rs9831409	0.85[EUR][1000 genomes]
rs9836178	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839035	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842974	0.83[EUR][1000 genomes]
rs9844736	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9846976	0.83[EUR][1000 genomes]
rs9847024	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9850563	0.81[ASN][1000 genomes]
rs9860296	0.86[ASN][1000 genomes]
rs9865094	0.83[EUR][1000 genomes]
rs9876403	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880978	0.80[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2336666	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2336666	MUSTN1	cis	Artery Aorta	GTEx
rs2336666	ITIH4-AS1	cis	lung	GTEx
rs2336666	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs2336666	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
3	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
4	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
7	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
11	chr3:52902200-52925200	Weak transcription	Placenta	Placenta
12	chr3:52904000-52918400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:52904600-52919400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52905000-52919800	Weak transcription	Right Ventricle	heart
15	chr3:52906000-52924400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:52908000-52915800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:52908000-52916200	Weak transcription	Aorta	Aorta
18	chr3:52908000-52924000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:52908000-52924000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:52908200-52919000	Weak transcription	NHEK	skin
21	chr3:52908200-52919600	Weak transcription	HSMM	muscle
22	chr3:52908200-52925400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52908200-52925400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:52908400-52924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:52908400-52924600	Weak transcription	NHLF	lung
26	chr3:52908400-52930600	Weak transcription	A549	lung
27	chr3:52908600-52916800	Weak transcription	Osteobl	bone
28	chr3:52908600-52924600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:52909200-52919400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:52909200-52920000	Weak transcription	Liver	Liver
32	chr3:52909200-52925200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52909600-52925400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52909800-52915800	Weak transcription	Primary T cells from cord blood	blood
35	chr3:52909800-52925200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:52909800-52925400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:52910000-52916200	Weak transcription	Psoas Muscle	Psoas
38	chr3:52910000-52918800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:52910000-52919400	Weak transcription	Dnd41	blood
40	chr3:52910000-52929400	Weak transcription	HMEC	breast
41	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:52910200-52920200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52910200-52925400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:52910400-52916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:52910400-52920200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:52910400-52924800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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