Variant report

Variant	rs4886864
Chromosome Location	chr15:77674022-77674023
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	chr15:77671092..77674187-chr15:77674414..77677871,3	K562	blood:
2	chr15:77673612..77675900-chr15:77720669..77722192,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10162742	0.85[YRI][hapmap]
rs10162778	0.80[ASN][1000 genomes]
rs11853696	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854466	0.83[ASN][1000 genomes]
rs11856084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11858844	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324016	0.90[ASN][1000 genomes]
rs12324211	0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12324632	0.87[YRI][hapmap]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912084	0.92[ASN][1000 genomes]
rs13380202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1374201	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.97[TSI][hapmap]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1493699	0.90[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs16968799	0.90[ASN][1000 genomes]
rs16968897	0.90[CEU][hapmap];0.82[YRI][hapmap]
rs17384809	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17385059	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17385352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17470529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470952	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17471252	0.85[ASN][1000 genomes]
rs17471431	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471480	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17471753	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17472200	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2012756	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2137977	0.83[ASN][1000 genomes]
rs2172587	0.90[ASN][1000 genomes]
rs2292594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437977	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs35651077	0.90[ASN][1000 genomes]
rs3784787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4886857	0.83[ASN][1000 genomes]
rs4886863	0.92[ASN][1000 genomes]
rs4886865	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59362734	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59386622	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60079927	0.83[ASN][1000 genomes]
rs62007297	0.90[ASN][1000 genomes]
rs62010566	0.90[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs74025105	0.83[ASN][1000 genomes]
rs74026910	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026912	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74026913	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026918	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026923	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74026925	0.82[EUR][1000 genomes]
rs8029163	0.80[ASN][1000 genomes]
rs8035526	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883627	0.83[JPT][hapmap]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1836778	chr15:77608747-77694607	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1795063	chr15:77628696-77697976	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2761954	chr15:77660345-77676969	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1793848	chr15:77662140-77676568	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1800929	chr15:77664889-77697976	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1792043	chr15:77664901-77708316	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4886864	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs4886864	HMG20A	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77639800-77687000	Weak transcription	Primary B cells from cord blood	blood
2	chr15:77645800-77677000	Weak transcription	Right Ventricle	heart
3	chr15:77647000-77687200	Weak transcription	A549	lung
4	chr15:77648600-77685800	Weak transcription	Gastric	stomach
5	chr15:77656200-77676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:77656400-77683200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:77662200-77677000	Weak transcription	NHDF-Ad	bronchial
8	chr15:77663000-77680200	Weak transcription	Osteobl	bone
9	chr15:77664600-77678200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:77665000-77676800	Weak transcription	Fetal Heart	heart
11	chr15:77669400-77683400	Weak transcription	Fetal Stomach	stomach
12	chr15:77670200-77676600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:77671400-77675800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:77671800-77677200	Weak transcription	Primary T cells from cord blood	blood
15	chr15:77672400-77674200	Enhancers	Left Ventricle	heart
16	chr15:77673200-77683400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:77673600-77674200	Enhancers	Right Atrium	heart
18	chr15:77673600-77675000	Enhancers	Spleen	Spleen
19	chr15:77673600-77676200	Weak transcription	Liver	Liver
20	chr15:77673800-77674200	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr15:77674000-77674200	Enhancers	Aorta	Aorta
22	chr15:77674000-77674200	Enhancers	Ovary	ovary
23	chr15:77674000-77674200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr15:77674000-77674800	Enhancers	Stomach Mucosa	stomach
25	chr15:77674000-77676000	Enhancers	Psoas Muscle	Psoas

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