Variant report

Variant	rs9883189
Chromosome Location	chr3:136289466-136289467
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	chr3:136288919..136291137-chr3:136468719..136471296,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs12695649	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062352	1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092193	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13314357	0.93[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs13316214	1.00[ASN][1000 genomes]
rs13321721	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433683	1.00[ASN][1000 genomes]
rs13433688	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs13434116	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604793	1.00[ASN][1000 genomes]
rs17298525	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17364492	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17365792	1.00[ASN][1000 genomes]
rs1872239	1.00[ASN][1000 genomes]
rs2176269	1.00[ASN][1000 genomes]
rs28390205	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472992	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634226	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs28641809	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28750366	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811905	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28877020	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34282798	1.00[ASN][1000 genomes]
rs34564818	1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34757183	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs34804893	0.93[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913797	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35096613	1.00[ASN][1000 genomes]
rs35100027	1.00[ASN][1000 genomes]
rs35198484	1.00[ASN][1000 genomes]
rs35210994	1.00[ASN][1000 genomes]
rs35326900	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	1.00[ASN][1000 genomes]
rs35428413	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880395	1.00[ASN][1000 genomes]
rs35899944	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	1.00[ASN][1000 genomes]
rs4038586	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509730	1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs67145204	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67382287	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767889	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768743	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6771002	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773949	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775314	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775466	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs67949818	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6806123	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336069	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336080	1.00[ASN][1000 genomes]
rs73230043	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612425	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9289513	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	1.00[ASN][1000 genomes]
rs9810789	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812579	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs9813115	1.00[ASN][1000 genomes]
rs9813376	1.00[ASN][1000 genomes]
rs9813691	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818536	1.00[ASN][1000 genomes]
rs9819856	1.00[ASN][1000 genomes]
rs9820717	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823373	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs9828088	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828976	1.00[ASN][1000 genomes]
rs9837158	1.00[ASN][1000 genomes]
rs9838884	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9839137	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9841529	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9845862	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9847427	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850364	1.00[ASN][1000 genomes]
rs9857833	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858560	1.00[ASN][1000 genomes]
rs9860879	1.00[ASN][1000 genomes]
rs9865995	1.00[ASN][1000 genomes]
rs9869630	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	1.00[ASN][1000 genomes]
rs9871184	1.00[ASN][1000 genomes]
rs9873536	1.00[ASN][1000 genomes]
rs9875770	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878078	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880211	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9881831	0.86[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9883189	PPP2R3A	cis	cerebellum	SCAN
rs9883189	PPP2R3A	cis	parietal	SCAN
rs9883189	GRK7	cis	cerebellum	SCAN
rs9883189	ERICH1	trans	parietal	SCAN

Chromatin state (count:77 , 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	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
6	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:136251600-136322400	Weak transcription	Liver	Liver
9	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
13	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:136265000-136294200	Weak transcription	Fetal Lung	lung
16	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:136266600-136291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:136266800-136291000	Weak transcription	Hela-S3	cervix
22	chr3:136266800-136291800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:136267000-136297800	Weak transcription	HUVEC	blood vessel
25	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
26	chr3:136268600-136292400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:136269000-136303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:136269600-136295800	Weak transcription	Fetal Heart	heart
29	chr3:136270400-136291600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
31	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:136273800-136290400	Weak transcription	Thymus	Thymus
33	chr3:136274200-136314000	Weak transcription	GM12878-XiMat	blood
34	chr3:136274800-136298000	Weak transcription	HSMM	muscle
35	chr3:136275200-136296400	Weak transcription	Pancreas	Pancrea
36	chr3:136276000-136290000	Weak transcription	Fetal Stomach	stomach
37	chr3:136276200-136290000	Weak transcription	Fetal Intestine Small	intestine
38	chr3:136276600-136303800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:136277200-136296200	Weak transcription	Psoas Muscle	Psoas
40	chr3:136277800-136315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:136279800-136303200	Weak transcription	Ovary	ovary
42	chr3:136280000-136323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:136280600-136292600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:136282400-136290600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:136283600-136295600	Weak transcription	A549	lung
46	chr3:136283600-136314600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
49	chr3:136285000-136307200	Weak transcription	Lung	lung
50	chr3:136285000-136314800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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