Variant report

Variant	rs7644471
Chromosome Location	chr3:136284561-136284562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10513016	1.00[CHB][hapmap]
rs12635723	0.89[YRI][hapmap]
rs13433980	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1484250	0.95[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17266364	1.00[CHB][hapmap]
rs17365351	1.00[CHB][hapmap]
rs17466223	1.00[CHB][hapmap]
rs28682370	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34804893	0.81[GIH][hapmap]
rs34962604	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34992220	0.81[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.89[YRI][hapmap]
rs35375192	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs35644083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931416	1.00[CHB][hapmap];0.85[LWK][hapmap]
rs3932048	0.95[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4336059	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4402873	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4678438	0.89[YRI][hapmap]
rs55993001	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56040643	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56047785	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56125228	0.82[AMR][1000 genomes]
rs59931907	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6439642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66810260	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6763239	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6765239	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6769934	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771713	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs6772759	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6773495	1.00[CHB][hapmap]
rs6773604	1.00[CHB][hapmap]
rs6782151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6788346	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6789329	0.86[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap]
rs6789541	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6789761	0.85[EUR][1000 genomes]
rs6799368	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6799699	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs6800969	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6804194	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs6806795	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612160	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7615706	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7621017	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7621970	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7623824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7626418	0.84[EUR][1000 genomes]
rs7627292	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7629905	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7644346	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7646563	1.00[CHB][hapmap]
rs7646723	1.00[CHB][hapmap]
rs7648591	0.82[AMR][1000 genomes]
rs923001	1.00[CHB][hapmap]
rs9812319	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9818372	0.86[EUR][1000 genomes]
rs9820513	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9828068	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9831321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9832572	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9834631	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839574	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9845762	0.89[YRI][hapmap]
rs9845950	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9858457	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs9866535	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868120	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9869361	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9869957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9876771	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9877786	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7644471	ZBTB38	cis	cerebellum	SCAN
rs7644471	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
7	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:136251600-136322400	Weak transcription	Liver	Liver
11	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
13	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:136265000-136294200	Weak transcription	Fetal Lung	lung
20	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:136266600-136284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:136266600-136284800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:136266600-136291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:136266800-136284600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:136266800-136291000	Weak transcription	Hela-S3	cervix
29	chr3:136266800-136291800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:136267000-136297800	Weak transcription	HUVEC	blood vessel
32	chr3:136267200-136284800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:136268000-136289400	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
35	chr3:136268400-136284600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:136268600-136292400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:136268800-136285000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:136269000-136303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:136269600-136295800	Weak transcription	Fetal Heart	heart
40	chr3:136270400-136291600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:136270800-136284600	Weak transcription	Fetal Thymus	thymus
42	chr3:136270800-136286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
44	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:136273800-136290400	Weak transcription	Thymus	Thymus
46	chr3:136274200-136314000	Weak transcription	GM12878-XiMat	blood
47	chr3:136274800-136298000	Weak transcription	HSMM	muscle
48	chr3:136275200-136296400	Weak transcription	Pancreas	Pancrea
49	chr3:136276000-136285000	Weak transcription	Fetal Intestine Large	intestine
50	chr3:136276000-136290000	Weak transcription	Fetal Stomach	stomach

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