Variant report

Variant	rs3959143
Chromosome Location	chr3:191118079-191118080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11542549	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1435062	0.96[ASN][1000 genomes]
rs1473869	0.90[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs1520203	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1609926	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16822378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16822382	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16848980	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs16866487	0.81[ASN][1000 genomes]
rs16866504	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs16866505	0.94[ASN][1000 genomes]
rs17753967	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17810246	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17810282	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17838893	0.81[ASN][1000 genomes]
rs2056333	0.81[ASN][1000 genomes]
rs2364379	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs28715898	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677632	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677725	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56174842	0.81[ASN][1000 genomes]
rs57211729	0.93[ASN][1000 genomes]
rs58141749	0.98[ASN][1000 genomes]
rs58645265	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59709586	0.96[ASN][1000 genomes]
rs61250936	0.94[ASN][1000 genomes]
rs6444541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73185209	0.84[ASN][1000 genomes]
rs73185210	0.86[ASN][1000 genomes]
rs73185213	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73185226	0.94[ASN][1000 genomes]
rs73185228	0.96[ASN][1000 genomes]
rs73185240	0.98[ASN][1000 genomes]
rs73185255	0.98[ASN][1000 genomes]
rs73185263	0.99[ASN][1000 genomes]
rs73185284	0.95[ASN][1000 genomes]
rs73185287	0.95[ASN][1000 genomes]
rs73185288	0.93[ASN][1000 genomes]
rs7637196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642387	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648886	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9290986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823680	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824437	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839751	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843934	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853569	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863255	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876944	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3959143	PIGX	cis	cerebellum	SCAN
rs3959143	CCDC50	cis	Thyroid	GTEx
rs3959143	CCDC50	cis	Artery Tibial	GTEx
rs3959143	ADA	trans	cerebellum	SCAN
rs3959143	PPP1R2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
10	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
11	chr3:191100200-191119600	Weak transcription	K562	blood
12	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
13	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
14	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
15	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
17	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:191112200-191118400	Strong transcription	NH-A	brain
20	chr3:191113200-191118200	Weak transcription	Hela-S3	cervix
21	chr3:191113600-191118200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:191114200-191119400	Weak transcription	NHLF	lung
25	chr3:191114400-191119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:191114400-191119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:191114400-191120400	Weak transcription	HSMM	muscle
28	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:191114400-191121400	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:191114600-191118200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:191115400-191118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:191116000-191119800	Weak transcription	Left Ventricle	heart
33	chr3:191116000-191119800	Weak transcription	Ovary	ovary
34	chr3:191116000-191121200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:191116000-191121600	Weak transcription	Primary B cells from cord blood	blood
36	chr3:191116400-191118800	Weak transcription	Placenta	Placenta
37	chr3:191116600-191118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:191116600-191118800	Weak transcription	Osteobl	bone
39	chr3:191116600-191119600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:191116600-191119600	Weak transcription	Liver	Liver
41	chr3:191117000-191118600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:191117000-191118600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:191117200-191127200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:191117200-191127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:191117400-191118400	ZNF genes & repeats	Lung	lung
46	chr3:191117800-191118200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:191117800-191118400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:191117800-191118400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:191117800-191118400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:191117800-191119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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