Variant report

Variant	rs1536192
Chromosome Location	chr13:50120985-50120986
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	chr13:50119828..50121736-chr13:50158802..50160343,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1198422	0.90[JPT][hapmap]
rs1359542	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1536195	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570884	0.85[CEU][hapmap]
rs1886793	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1977353	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1998780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104183	0.92[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2146145	0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2274278	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897741	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941648	0.86[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4941650	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs5007254	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6561539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561540	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561542	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139724	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7317140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324024	0.86[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7325207	0.89[EUR][1000 genomes]
rs7983283	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7986405	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7989286	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7992396	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7992691	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7996012	0.85[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8000962	0.81[EUR][1000 genomes]
rs9526577	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535259	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535262	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535269	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9562896	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	nsv1052801	chr13:50116407-50144995	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1536192	ARL11	cis	parietal	SCAN
rs1536192	RCBTB1	cis	cerebellum	SCAN
rs1536192	RCBTB1	cis	parietal	SCAN
rs1536192	CAB39L	cis	cerebellum	SCAN
rs1536192	PHF11	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
3	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
4	chr13:50090000-50122800	Weak transcription	Ovary	ovary
5	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
6	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
8	chr13:50097800-50135000	Weak transcription	Colonic Mucosa	Colon
9	chr13:50101600-50142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:50104600-50143800	Weak transcription	Hela-S3	cervix
11	chr13:50106600-50133200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:50109200-50121600	Weak transcription	Brain Germinal Matrix	brain
14	chr13:50110400-50134400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:50110600-50124800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:50110800-50126800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr13:50111400-50127600	Weak transcription	Fetal Heart	heart
18	chr13:50111600-50136600	Strong transcription	Dnd41	blood
19	chr13:50111800-50133200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:50112000-50135000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:50112200-50121200	Strong transcription	Fetal Intestine Large	intestine
22	chr13:50112200-50134200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:50112200-50138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr13:50113200-50121400	Strong transcription	HMEC	breast
25	chr13:50113200-50127200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:50113600-50123400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:50114000-50125800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr13:50114000-50126600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:50115000-50123400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:50115000-50123400	Weak transcription	NHLF	lung
31	chr13:50115000-50123600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:50115000-50123800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr13:50115000-50132200	Weak transcription	Colon Smooth Muscle	Colon
34	chr13:50115000-50140400	Weak transcription	Fetal Brain Male	brain
35	chr13:50115200-50122600	Weak transcription	Fetal Lung	lung
36	chr13:50115200-50124600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr13:50115200-50124800	Weak transcription	Fetal Brain Female	brain
38	chr13:50115200-50132800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr13:50115200-50133200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr13:50115200-50135000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr13:50115200-50135600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr13:50115200-50140400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr13:50115400-50123400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:50115400-50124000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr13:50115400-50124400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr13:50115400-50126200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:50115400-50130800	Weak transcription	NH-A	brain
48	chr13:50115400-50131200	Weak transcription	HSMM	muscle
49	chr13:50115400-50133200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr13:50115400-50141200	Weak transcription	K562	blood

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