Variant report

Variant	rs9812319
Chromosome Location	chr3:136238860-136238861
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	chr3:136223066..136225762-chr3:136237795..136239369,2	MCF-7	breast:
2	chr3:136237342..136239151-chr3:136470510..136472888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12635723	0.84[LWK][hapmap];0.85[YRI][hapmap]
rs13433980	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs1484250	0.95[CEU][hapmap];0.92[YRI][hapmap]
rs16843991	0.95[CEU][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28396702	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34165586	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34962604	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35375192	1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35644083	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3732519	1.00[CHD][hapmap]
rs3821444	1.00[CHD][hapmap]
rs3932048	0.95[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4336059	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs4402873	0.83[EUR][1000 genomes]
rs4678438	0.85[YRI][hapmap]
rs55993001	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56040643	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56047785	0.84[EUR][1000 genomes]
rs56125228	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56251259	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59931907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6439638	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs6439642	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66810260	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6765239	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs6766450	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769934	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776841	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs6782151	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6783337	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs6789541	0.83[EUR][1000 genomes]
rs6789761	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6799368	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800969	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs6804194	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6806795	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs699165	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs7612160	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615706	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620314	0.93[LWK][hapmap];0.88[MKK][hapmap]
rs7621017	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621970	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623824	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs7627292	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7644346	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs7644471	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]
rs7648591	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9809184	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9812513	1.00[CEU][hapmap]
rs9819496	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9820513	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs9831321	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9832572	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9834631	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9839574	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs9845762	0.80[LWK][hapmap];0.85[YRI][hapmap]
rs9845950	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs9850383	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9853387	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9854084	0.82[YRI][hapmap]
rs9858457	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9860801	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9866535	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868120	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9869957	0.95[CEU][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
rs9812319	ZBTB38	cis	cerebellum	SCAN
rs9812319	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:65 , 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	chr3:136176600-136240000	Weak transcription	HMEC	breast
3	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
5	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:136195400-136241800	Weak transcription	NH-A	brain
9	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:136212400-136249600	Weak transcription	Lung	lung
14	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
15	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
18	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136215600-136246200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:136220600-136240000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:136220600-136242800	Weak transcription	GM12878-XiMat	blood
26	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:136221000-136246400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:136221200-136241200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:136221200-136251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:136221400-136246400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:136221400-136251000	Weak transcription	Liver	Liver
32	chr3:136221600-136246200	Weak transcription	Fetal Intestine Large	intestine
33	chr3:136221600-136251000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:136222000-136246200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:136222000-136246600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:136222200-136251000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:136222200-136251200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:136222400-136266200	Weak transcription	HSMM	muscle
39	chr3:136227800-136246600	Weak transcription	Fetal Thymus	thymus
40	chr3:136227800-136246600	Weak transcription	Thymus	Thymus
41	chr3:136230000-136246400	Weak transcription	Fetal Stomach	stomach
42	chr3:136230400-136251000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:136230600-136247600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:136230800-136246200	Weak transcription	Fetal Lung	lung
45	chr3:136232000-136241800	Weak transcription	Osteobl	bone
46	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:136232200-136246600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:136232200-136247000	Weak transcription	Aorta	Aorta
49	chr3:136232400-136251000	Weak transcription	Adipose Nuclei	Adipose
50	chr3:136232400-136255200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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