Variant report

Variant	rs1925742
Chromosome Location	chr13:50109584-50109585
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	chr13:50060673..50063121-chr13:50108619..50111227,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236577	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1046027	0.81[ASW][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs1046028	0.87[ASW][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs1046295	0.81[ASW][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs1062979	0.81[ASN][1000 genomes]
rs12146924	0.88[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs17073051	0.83[JPT][hapmap];0.81[YRI][hapmap]
rs1977352	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2038881	0.88[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs2407696	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2980	0.95[JPT][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap]
rs2981	0.95[JPT][hapmap];0.81[MKK][hapmap]
rs3186012	0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs3186013	0.87[ASW][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs3186024	0.87[ASW][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs3751384	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3794377	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829366	0.81[ASW][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs4085853	0.84[AMR][1000 genomes]
rs4942838	0.81[ASN][1000 genomes]
rs4942839	0.81[ASN][1000 genomes]
rs4942840	0.81[ASN][1000 genomes]
rs4942843	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942848	0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs6561534	0.81[ASW][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs7139494	0.95[JPT][hapmap]
rs7317982	0.86[ASW][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.81[ASN][1000 genomes]
rs7322077	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7323716	0.81[ASW][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs7331262	0.81[ASN][1000 genomes]
rs7331330	0.81[ASN][1000 genomes]
rs7333969	0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7982445	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982555	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982964	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7983291	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7989504	0.81[ASN][1000 genomes]
rs7990988	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs7991031	0.95[JPT][hapmap];0.84[MKK][hapmap]
rs7995684	0.87[ASW][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs7996207	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7999363	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526567	0.94[JPT][hapmap]
rs9535254	0.95[JPT][hapmap];0.85[YRI][hapmap]
rs9535255	0.95[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs9535256	0.80[ASN][1000 genomes]
rs9535257	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1925742	RCBTB1	cis	cerebellum	SCAN
rs1925742	RCBTB1	cis	parietal	SCAN
rs1925742	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50086400-50113600	Weak transcription	Brain Angular Gyrus	brain
4	chr13:50086600-50114200	Weak transcription	Fetal Brain Female	brain
5	chr13:50088200-50113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
7	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
8	chr13:50089400-50114200	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:50090000-50113600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:50090000-50122800	Weak transcription	Ovary	ovary
11	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
12	chr13:50090200-50114200	Weak transcription	Aorta	Aorta
13	chr13:50090200-50117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:50090400-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:50090400-50114200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:50091000-50114200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:50092000-50112200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:50092000-50114200	Weak transcription	Fetal Brain Male	brain
20	chr13:50092200-50113400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:50093800-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr13:50094000-50112000	Weak transcription	HSMMtube	muscle
23	chr13:50094000-50114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:50094600-50113600	Weak transcription	Gastric	stomach
25	chr13:50094600-50113800	Weak transcription	Pancreas	Pancrea
26	chr13:50094600-50120000	Weak transcription	Spleen	Spleen
27	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
28	chr13:50095000-50120400	Weak transcription	A549	lung
29	chr13:50097600-50113600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:50097600-50114000	Weak transcription	Fetal Lung	lung
31	chr13:50097800-50113400	Weak transcription	NHLF	lung
32	chr13:50097800-50113600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:50097800-50135000	Weak transcription	Colonic Mucosa	Colon
34	chr13:50098000-50114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr13:50098200-50114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:50100200-50112200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:50101000-50110400	Weak transcription	Fetal Intestine Small	intestine
38	chr13:50101600-50114200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr13:50101600-50114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:50101600-50142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:50101800-50114000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:50102400-50113400	Weak transcription	Osteobl	bone
43	chr13:50102600-50110000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:50102600-50113600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:50103000-50113200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr13:50103200-50113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr13:50103200-50114400	Weak transcription	NH-A	brain
48	chr13:50103400-50109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr13:50103400-50111800	Weak transcription	HSMM	muscle
50	chr13:50103400-50114200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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