Variant report

Variant	rs4886509
Chromosome Location	chr15:77354847-77354848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77346809..77348699-chr15:77354640..77356217,2	MCF-7	breast:
2	chr15:77354730..77357508-chr15:77359818..77362663,2	MCF-7	breast:
3	chr15:77336838..77340785-chr15:77352977..77355906,3	K562	blood:

Variant related genes	Relation type
ENSG00000269951	Chromatin interaction
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072641	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11630497	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636613	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636648	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148761	0.96[CEU][hapmap]
rs12372961	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12438566	0.80[MEX][hapmap]
rs12901188	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912792	0.83[ASN][1000 genomes]
rs16968665	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404233	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs2404234	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34443712	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935339	0.87[JPT][hapmap]
rs4078354	0.87[CEU][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs4886847	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55645420	0.83[ASN][1000 genomes]
rs7166154	0.96[CEU][hapmap]
rs7169831	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177533	0.81[CHB][hapmap]
rs8032	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806416	0.87[CEU][hapmap]

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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4886509	ISL2	cis	cerebellum	SCAN
rs4886509	RP11-797A18.4	cis	Muscle Skeletal	GTEx
rs4886509	PSTPIP1	cis	lymphoblastoid	seeQTL
rs4886509	TSPAN3	cis	cerebellum	SCAN
rs4886509	RP11-797A18.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77321200-77362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:77339000-77362000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77339200-77358000	Weak transcription	Colonic Mucosa	Colon
4	chr15:77339400-77359200	Weak transcription	Right Ventricle	heart
5	chr15:77345000-77355200	Weak transcription	HMEC	breast
6	chr15:77345200-77360200	Weak transcription	Spleen	Spleen
7	chr15:77345200-77362000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:77345400-77355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:77345400-77361400	Weak transcription	Placenta	Placenta
10	chr15:77346600-77358600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:77346600-77359800	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr15:77346600-77361200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:77346800-77356200	Weak transcription	Hela-S3	cervix
14	chr15:77347200-77361600	Weak transcription	Dnd41	blood
15	chr15:77347400-77358600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:77349000-77357600	Enhancers	Liver	Liver
17	chr15:77349200-77362000	Weak transcription	Lung	lung
18	chr15:77349400-77361000	Weak transcription	Fetal Thymus	thymus
19	chr15:77349600-77356200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:77349600-77357800	Enhancers	Fetal Intestine Small	intestine
21	chr15:77349600-77358600	Weak transcription	Gastric	stomach
22	chr15:77349600-77362000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:77351000-77361800	Weak transcription	Pancreas	Pancrea
24	chr15:77351200-77356200	Weak transcription	HepG2	liver
25	chr15:77351600-77355000	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:77351800-77355000	Enhancers	Brain Hippocampus Middle	brain
27	chr15:77351800-77355000	Enhancers	Colon Smooth Muscle	Colon
28	chr15:77351800-77355600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:77352200-77355200	Enhancers	Brain Germinal Matrix	brain
30	chr15:77352400-77362000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:77352600-77356600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:77352600-77359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77352600-77360200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:77352600-77362000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:77353000-77355000	Enhancers	Fetal Heart	heart
36	chr15:77353000-77356000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:77353000-77356000	Weak transcription	Brain Substantia Nigra	brain
38	chr15:77353000-77359200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:77353000-77361800	Weak transcription	Thymus	Thymus
40	chr15:77353200-77355000	Enhancers	Fetal Lung	lung
41	chr15:77353200-77356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:77353200-77356000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:77353200-77356000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:77353200-77356000	Weak transcription	A549	lung
45	chr15:77353200-77356200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:77353200-77356200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:77353200-77356600	Weak transcription	Primary B cells from cord blood	blood
48	chr15:77353200-77356800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:77353200-77356800	Weak transcription	Small Intestine	intestine
50	chr15:77353200-77357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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