Variant report

Variant	rs9823373
Chromosome Location	chr3:136167027-136167028
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	chr3:136166580..136169214-chr3:136176961..136178739,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12695645	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695649	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs13072038	1.00[ASN][1000 genomes]
rs13092193	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316214	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321721	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs1604793	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200216	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17298525	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364492	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28634226	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28641809	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750366	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs28811905	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34031772	1.00[ASN][1000 genomes]
rs34135127	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs34168675	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34282798	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34324561	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34428695	1.00[ASN][1000 genomes]
rs34757183	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34804893	0.84[ASW][hapmap];0.93[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs34913797	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35326900	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	1.00[ASN][1000 genomes]
rs35522825	1.00[ASN][1000 genomes]
rs35899944	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs6768743	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771002	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773949	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	1.00[ASN][1000 genomes]
rs6775466	0.85[LWK][hapmap]
rs6790083	0.85[LWK][hapmap]
rs67949818	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796523	0.80[EUR][1000 genomes]
rs6806123	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs7612425	1.00[ASN][1000 genomes]
rs9810051	0.83[EUR][1000 genomes]
rs9810789	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812579	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813115	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813691	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs9818056	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818536	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820621	0.83[EUR][1000 genomes]
rs9820717	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs9826454	1.00[ASN][1000 genomes]
rs9828088	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832813	0.92[MEX][hapmap]
rs9837158	0.86[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841529	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844666	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs9847427	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9857966	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs9866840	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869630	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872178	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878078	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880211	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9881831	1.00[ASN][1000 genomes]
rs9883189	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]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9823373	NCK1	cis	cerebellum	SCAN
rs9823373	PPP2R3A	cis	cerebellum	SCAN
rs9823373	ERICH1	trans	parietal	SCAN
rs9823373	PPP2R3A	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
6	chr3:136112200-136174200	Weak transcription	Osteobl	bone
7	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
8	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
11	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
14	chr3:136131400-136175400	Weak transcription	HMEC	breast
15	chr3:136133200-136173800	Weak transcription	Fetal Heart	heart
16	chr3:136133600-136173400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:136135200-136173400	Weak transcription	NHEK	skin
18	chr3:136138200-136173600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:136138800-136171400	Weak transcription	HepG2	liver
20	chr3:136138800-136174200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:136139800-136175400	Weak transcription	Small Intestine	intestine
22	chr3:136139800-136175800	Weak transcription	Right Ventricle	heart
23	chr3:136140000-136168200	Weak transcription	NH-A	brain
24	chr3:136140000-136169200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:136140000-136169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:136140000-136174200	Weak transcription	Pancreas	Pancrea
27	chr3:136140000-136175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:136143200-136174000	Weak transcription	GM12878-XiMat	blood
29	chr3:136148000-136174400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:136152600-136168400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:136152600-136168800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:136152600-136169000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:136158400-136169000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:136158800-136174400	Weak transcription	NHDF-Ad	bronchial
35	chr3:136160600-136174000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:136160600-136174200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:136161000-136170400	Weak transcription	Lung	lung
38	chr3:136161000-136172800	Weak transcription	Fetal Brain Female	brain
39	chr3:136161000-136173200	Weak transcription	Brain Germinal Matrix	brain
40	chr3:136161000-136174000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:136161000-136176000	Weak transcription	NHLF	lung
42	chr3:136161200-136169000	Weak transcription	Brain Substantia Nigra	brain
43	chr3:136161200-136173600	Weak transcription	Fetal Kidney	kidney
44	chr3:136161200-136174200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:136161200-136175000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:136161400-136169600	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:136161400-136172800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:136161400-136173400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:136161600-136169000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:136161600-136169600	Weak transcription	Fetal Lung	lung

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