Variant report

Variant	rs4886857
Chromosome Location	chr15:77576567-77576568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1015813	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11853625	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11853633	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11853696	0.81[ASN][1000 genomes]
rs11854182	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11854466	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856538	0.96[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11857804	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324211	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs12902446	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13380152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13380202	0.85[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];0.81[LWK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs17381652	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17383078	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17384809	0.85[ASN][1000 genomes]
rs17385059	0.85[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17385352	0.85[ASN][1000 genomes]
rs17468413	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17470529	0.83[ASN][1000 genomes]
rs17470952	0.81[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];0.84[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap]
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]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs2137977	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs28437977	0.83[ASN][1000 genomes]
rs2864079	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3784787	0.83[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4638539	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886864	0.83[ASN][1000 genomes]
rs4886865	0.83[ASN][1000 genomes]
rs55881066	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56070388	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58792939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59831220	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60079927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60761381	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60863150	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163620	0.93[ASN][1000 genomes]
rs7173670	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025074	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74025104	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74025105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74026913	0.80[ASN][1000 genomes]
rs74027548	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027549	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7496431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8035526	0.83[ASN][1000 genomes]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9806326	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	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
11	nsv869991	chr15:77545316-77578885	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv33934	chr15:77548764-77579524	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886857	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs4886857	HMG20A	cis	parietal	SCAN
rs4886857	CRABP1	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
2	chr15:77528800-77577200	Weak transcription	Spleen	Spleen
3	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
4	chr15:77541800-77589800	Weak transcription	Fetal Intestine Small	intestine
5	chr15:77542200-77580000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:77544400-77581000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:77544600-77589200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:77559400-77578800	Weak transcription	Ovary	ovary
9	chr15:77559600-77578800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:77559800-77579400	Weak transcription	Brain Anterior Caudate	brain
11	chr15:77559800-77585200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:77560000-77576600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:77562000-77580200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:77562200-77589600	Weak transcription	Primary T cells from cord blood	blood
15	chr15:77563400-77577400	Weak transcription	Fetal Kidney	kidney
16	chr15:77565400-77578800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:77567600-77580200	Weak transcription	Fetal Lung	lung
18	chr15:77568400-77578600	Weak transcription	Esophagus	oesophagus
19	chr15:77568800-77578000	Weak transcription	Thymus	Thymus
20	chr15:77570000-77579400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:77571800-77578800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:77571800-77579400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:77571800-77579600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:77571800-77585600	Weak transcription	Right Ventricle	heart
25	chr15:77572000-77578600	Weak transcription	Placenta	Placenta
26	chr15:77572000-77582000	Weak transcription	Left Ventricle	heart
27	chr15:77572200-77580000	Weak transcription	HSMMtube	muscle
28	chr15:77572600-77580800	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:77573000-77577800	Weak transcription	K562	blood
30	chr15:77573600-77578600	Weak transcription	Primary B cells from cord blood	blood
31	chr15:77573600-77580600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:77573600-77589400	Weak transcription	Fetal Stomach	stomach
33	chr15:77574000-77576800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr15:77574200-77577000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:77574400-77576600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr15:77574400-77577000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:77574600-77580800	Weak transcription	Fetal Brain Male	brain
38	chr15:77574600-77585200	Weak transcription	Psoas Muscle	Psoas
39	chr15:77575000-77585400	Weak transcription	NH-A	brain
40	chr15:77575200-77576800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:77575200-77577200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:77575200-77577800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:77575400-77577000	Strong transcription	HUVEC	blood vessel
44	chr15:77575400-77577600	Weak transcription	Brain Substantia Nigra	brain
45	chr15:77575400-77580400	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:77575400-77586000	Weak transcription	HepG2	liver
47	chr15:77575600-77579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:77575600-77579400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:77575600-77580000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:77576000-77577600	Strong transcription	Dnd41	blood

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