Variant report

Variant	rs13071931
Chromosome Location	chr3:50062878-50062879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50037509..50039299-chr3:50062748..50064702,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1061474	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs1138536	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs11709573	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs12637671	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13067082	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13095697	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13097720	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs14321	1.00[CHD][hapmap]
rs17304079	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17657664	0.83[LWK][hapmap];0.94[YRI][hapmap]
rs1996663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1996664	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs2014004	0.88[YRI][hapmap]
rs2526397	1.00[CHD][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap]
rs2526747	0.91[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2624826	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs35012435	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35375092	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35491931	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35849525	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774734	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs3774759	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs4688754	0.81[AFR][1000 genomes]
rs55924524	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62262106	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62262118	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62263602	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6446195	0.81[AFR][1000 genomes]
rs6762477	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs6785500	0.81[YRI][hapmap]
rs6787892	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7061	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs71326904	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71326915	0.80[EUR][1000 genomes]
rs7615206	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs7615318	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627864	1.00[YRI][hapmap]
rs7635601	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7648652	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs868891	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs9682295	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv3425363	chr3:50056273-50063031	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13071931	RNF123	cis	parietal	SCAN
rs13071931	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13071931	RBM6	cis	cerebellum	SCAN
rs13071931	QRICH1	cis	cerebellum	SCAN
rs13071931	RBM6	cis	Artery Tibial	GTEx
rs13071931	ARIH2	cis	cerebellum	SCAN
rs13071931	GNL3	cis	parietal	SCAN
rs13071931	RBM6	cis	Whole Blood	GTEx
rs13071931	ITIH3	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
4	chr3:50010800-50087000	Weak transcription	NHLF	lung
5	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
7	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
9	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
10	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
11	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
17	chr3:50041600-50065200	Weak transcription	NH-A	brain
18	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
19	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
20	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
22	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:50046800-50064600	Weak transcription	Aorta	Aorta
25	chr3:50046800-50065400	Weak transcription	Fetal Kidney	kidney
26	chr3:50046800-50085800	Weak transcription	HMEC	breast
27	chr3:50047200-50085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:50047200-50085400	Weak transcription	Left Ventricle	heart
29	chr3:50047200-50092600	Weak transcription	Gastric	stomach
30	chr3:50047400-50085000	Weak transcription	Lung	lung
31	chr3:50048800-50085600	Weak transcription	A549	lung
32	chr3:50049800-50084000	Weak transcription	Brain Germinal Matrix	brain
33	chr3:50050600-50066000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:50051400-50084600	Weak transcription	Spleen	Spleen
35	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
36	chr3:50051800-50085000	Weak transcription	Brain Anterior Caudate	brain
37	chr3:50051800-50085400	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:50052200-50084800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:50052200-50087000	Weak transcription	NHDF-Ad	bronchial
40	chr3:50052400-50085600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:50053200-50064800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:50053200-50065600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:50055600-50084200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:50055600-50085600	Weak transcription	Hela-S3	cervix
45	chr3:50056000-50066000	Strong transcription	Fetal Thymus	thymus
46	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:50056800-50078400	Weak transcription	Ovary	ovary
48	chr3:50057000-50071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:50057000-50073400	Weak transcription	Thymus	Thymus
50	chr3:50057000-50085400	Weak transcription	Fetal Lung	lung

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