Variant report

Variant	rs1346719
Chromosome Location	chr3:53077372-53077373
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	chr3:53060296..53062382-chr3:53075868..53077771,2	MCF-7	breast:
2	chr3:53059584..53062030-chr3:53075790..53077753,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10510761	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11707575	0.94[EUR][1000 genomes]
rs11707780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710292	0.94[EUR][1000 genomes]
rs11710394	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11710707	0.89[EUR][1000 genomes]
rs11711773	0.93[EUR][1000 genomes]
rs11712653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs11713171	1.00[EUR][1000 genomes]
rs11713206	0.89[EUR][1000 genomes]
rs11713290	0.89[EUR][1000 genomes]
rs11713859	0.93[EUR][1000 genomes]
rs11713926	0.85[JPT][hapmap]
rs11714037	0.89[EUR][1000 genomes]
rs11714876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714902	0.94[EUR][1000 genomes]
rs11715231	0.84[EUR][1000 genomes]
rs11717132	0.89[EUR][1000 genomes]
rs11717619	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11717715	0.89[EUR][1000 genomes]
rs11718388	1.00[EUR][1000 genomes]
rs11718538	0.87[EUR][1000 genomes]
rs11718752	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11718834	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11720191	0.89[EUR][1000 genomes]
rs13058817	0.93[EUR][1000 genomes]
rs13069006	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13072395	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13072457	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs13072818	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs13074524	0.89[EUR][1000 genomes]
rs13076033	0.91[CEU][hapmap]
rs13078834	0.89[EUR][1000 genomes]
rs13078971	0.94[EUR][1000 genomes]
rs13084937	0.94[EUR][1000 genomes]
rs13085514	0.94[EUR][1000 genomes]
rs13085544	0.91[EUR][1000 genomes]
rs13088281	0.85[JPT][hapmap]
rs13091844	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13092352	0.87[EUR][1000 genomes]
rs13320044	0.94[EUR][1000 genomes]
rs1560333	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17052727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336540	0.89[EUR][1000 genomes]
rs2336541	0.89[EUR][1000 genomes]
rs2564926	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2564941	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581807	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3097417	0.93[EUR][1000 genomes]
rs34121720	1.00[EUR][1000 genomes]
rs34238610	0.95[EUR][1000 genomes]
rs34244302	0.94[EUR][1000 genomes]
rs34313969	0.89[EUR][1000 genomes]
rs34340609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34493168	0.89[EUR][1000 genomes]
rs34754279	0.89[EUR][1000 genomes]
rs34872575	0.89[EUR][1000 genomes]
rs34933390	0.89[EUR][1000 genomes]
rs34943350	0.89[EUR][1000 genomes]
rs34979715	0.95[EUR][1000 genomes]
rs35076015	0.95[EUR][1000 genomes]
rs35163227	0.94[EUR][1000 genomes]
rs35174175	0.95[EUR][1000 genomes]
rs35230793	0.84[EUR][1000 genomes]
rs35378159	0.89[EUR][1000 genomes]
rs35384050	0.89[EUR][1000 genomes]
rs35385050	0.89[EUR][1000 genomes]
rs35507120	0.95[EUR][1000 genomes]
rs35720014	0.89[EUR][1000 genomes]
rs35737577	0.89[EUR][1000 genomes]
rs35849389	0.89[EUR][1000 genomes]
rs36090694	0.89[EUR][1000 genomes]
rs3796352	1.00[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3806692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478072	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs58515094	0.89[EUR][1000 genomes]
rs58660500	1.00[EUR][1000 genomes]
rs59583591	0.94[EUR][1000 genomes]
rs60887045	0.89[EUR][1000 genomes]
rs60942590	0.89[EUR][1000 genomes]
rs61172708	0.89[EUR][1000 genomes]
rs6445555	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445556	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445557	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71299622	0.84[EUR][1000 genomes]
rs71299700	0.81[EUR][1000 genomes]
rs71301804	0.98[EUR][1000 genomes]
rs71301808	1.00[EUR][1000 genomes]
rs71301809	0.94[EUR][1000 genomes]
rs71301811	0.93[EUR][1000 genomes]
rs71301814	0.94[EUR][1000 genomes]
rs71617204	0.95[EUR][1000 genomes]
rs750474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7622420	0.94[EUR][1000 genomes]
rs7625448	0.94[EUR][1000 genomes]
rs7640293	0.94[EUR][1000 genomes]
rs7645611	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs9756317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875573	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv590341	chr3:53077372-53079522	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv590342	chr3:53077372-53079888	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1346719	ITIH4	cis	multi-tissue	Pritchard
rs1346719	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs1346719	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
2	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:53056600-53077800	Weak transcription	Fetal Stomach	stomach
4	chr3:53064000-53078400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:53065400-53077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:53065400-53078600	Weak transcription	Gastric	stomach
7	chr3:53068000-53077600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:53068800-53077400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:53069200-53077800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:53069200-53077800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:53069800-53077600	Weak transcription	Stomach Mucosa	stomach
12	chr3:53070200-53077800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:53071000-53078400	Weak transcription	Right Ventricle	heart
14	chr3:53071000-53078600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:53071400-53077800	Weak transcription	Left Ventricle	heart
16	chr3:53072800-53077800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:53073000-53077800	Weak transcription	Fetal Brain Female	brain
18	chr3:53073200-53077800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:53073200-53078400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:53073200-53078400	Weak transcription	NHLF	lung
21	chr3:53073400-53078200	Weak transcription	HSMM	muscle
22	chr3:53073800-53077800	Weak transcription	Psoas Muscle	Psoas
23	chr3:53073800-53078400	Weak transcription	Pancreas	Pancrea
24	chr3:53074000-53077400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:53074600-53078200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:53074600-53078200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:53074800-53077800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:53074800-53077800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:53074800-53077800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:53074800-53077800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:53074800-53077800	Weak transcription	Hela-S3	cervix
32	chr3:53074800-53078200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:53074800-53078200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:53074800-53078200	Weak transcription	NH-A	brain
35	chr3:53074800-53078200	Weak transcription	NHDF-Ad	bronchial
36	chr3:53074800-53078400	Weak transcription	HSMMtube	muscle
37	chr3:53075000-53077800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:53075000-53077800	Weak transcription	Osteobl	bone
39	chr3:53075000-53078400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:53075200-53077600	Weak transcription	Fetal Intestine Small	intestine
41	chr3:53075200-53077800	Weak transcription	Fetal Intestine Large	intestine
42	chr3:53075200-53078200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:53075400-53077800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:53075400-53077800	Weak transcription	HMEC	breast
45	chr3:53075400-53077800	Weak transcription	NHEK	skin
46	chr3:53075400-53078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:53075600-53078200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:53076000-53077800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:53076200-53077600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:53076200-53077600	Enhancers	Dnd41	blood

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