Variant report

Variant	rs4678432
Chromosome Location	chr3:135720241-135720242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12630389	0.90[ASN][1000 genomes]
rs12632791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12633805	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12637541	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059064	0.87[ASN][1000 genomes]
rs13065499	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072690	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13072782	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13075579	0.98[ASN][1000 genomes]
rs13078865	0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13084404	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13092707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13097172	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13097176	0.81[ASN][1000 genomes]
rs13097267	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13100235	0.84[ASN][1000 genomes]
rs1523593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1523598	0.81[ASN][1000 genomes]
rs1523599	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523600	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16843560	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16843611	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140450	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2177407	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2400649	0.87[ASN][1000 genomes]
rs34447526	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34683314	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34706807	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35097316	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35209948	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35264626	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35532770	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35946332	0.87[ASN][1000 genomes]
rs35961065	0.90[ASN][1000 genomes]
rs3946444	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4075999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331626	0.86[ASN][1000 genomes]
rs4678224	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4678288	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678435	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55873361	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56152207	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57594457	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60070757	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61791712	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61791714	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439603	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6439605	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6439609	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439610	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6439614	0.86[ASN][1000 genomes]
rs6439615	0.87[ASN][1000 genomes]
rs6439618	0.87[ASN][1000 genomes]
rs6439622	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6439623	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs6439624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770366	0.85[ASN][1000 genomes]
rs6771950	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775261	0.87[ASN][1000 genomes]
rs6779903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793273	0.86[ASN][1000 genomes]
rs6803786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433592	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610302	0.87[ASN][1000 genomes]
rs7625177	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7625607	0.88[ASN][1000 genomes]
rs7635621	0.87[ASN][1000 genomes]
rs7650079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289501	0.84[ASN][1000 genomes]
rs940229	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9682712	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9758578	0.95[ASN][1000 genomes]
rs9846554	0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9852009	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9852169	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9856799	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs9866235	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs9868239	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4678432	NCK1	cis	parietal	SCAN
rs4678432	SLC9A7	trans	cerebellum	SCAN
rs4678432	TMEM22	cis	cerebellum	SCAN
rs4678432	MSL2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
2	chr3:135701600-135720600	Weak transcription	Ovary	ovary
3	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:135710000-135726200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:135710000-135727200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:135710000-135737600	Weak transcription	Left Ventricle	heart
9	chr3:135710800-135727600	Weak transcription	Aorta	Aorta
10	chr3:135711600-135727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:135711600-135731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:135711800-135727000	Weak transcription	Pancreas	Pancrea
13	chr3:135711800-135727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:135711800-135730400	Weak transcription	HSMM	muscle
15	chr3:135711800-135730400	Weak transcription	Osteobl	bone
16	chr3:135711800-135737600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:135712400-135721800	Weak transcription	NHDF-Ad	bronchial
18	chr3:135714000-135721200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:135714000-135729200	Weak transcription	NH-A	brain
20	chr3:135714000-135735600	Weak transcription	Fetal Heart	heart
21	chr3:135714200-135726000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:135714200-135737600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:135714600-135726000	Weak transcription	Placenta	Placenta
24	chr3:135714800-135737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:135715000-135727000	Weak transcription	NHLF	lung
26	chr3:135715600-135732200	Weak transcription	Fetal Lung	lung
27	chr3:135715600-135737000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:135715600-135737600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:135716200-135736400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:135716600-135720400	Weak transcription	Gastric	stomach
31	chr3:135717000-135726200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:135717000-135726600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:135717000-135727000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:135717000-135730400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:135717200-135722200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:135717200-135725800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:135717200-135726000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:135717200-135727600	Weak transcription	Fetal Stomach	stomach
39	chr3:135717200-135737600	Weak transcription	NHEK	skin
40	chr3:135717200-135747000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:135717400-135735200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:135717800-135737400	Weak transcription	HSMMtube	muscle
43	chr3:135718000-135727200	Weak transcription	Psoas Muscle	Psoas
44	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
45	chr3:135718200-135736600	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:135718400-135737200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:135718600-135727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:135718800-135737600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:135719000-135720400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:135719000-135730400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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