Variant report

Variant	rs4886862
Chromosome Location	chr15:77652368-77652369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1005752	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10152181	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1022172	0.93[ASN][1000 genomes]
rs11072653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632941	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs11632966	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633054	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11636554	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11857294	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857450	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs11857860	0.81[JPT][hapmap]
rs11858641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1191196	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324627	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs12901130	0.89[JPT][hapmap]
rs12901503	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12904938	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12905951	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906708	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909924	0.82[ASN][1000 genomes]
rs12910361	0.90[ASN][1000 genomes]
rs12910480	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911371	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912050	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913233	0.81[ASN][1000 genomes]
rs12914345	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389436	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493700	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1565757	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602925	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055901	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs2175941	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28584877	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34591043	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4243045	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs4886515	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886858	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886869	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4886875	0.81[JPT][hapmap]
rs4886876	0.81[JPT][hapmap]
rs4886877	0.81[JPT][hapmap]
rs59153558	0.84[ASN][1000 genomes]
rs62007299	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62008452	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495237	0.80[ASN][1000 genomes]
rs6495240	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs7119	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs7163503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7166927	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167794	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175674	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176302	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178572	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs8024485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8030074	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034133	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs8037426	0.80[ASN][1000 genomes]
rs8037561	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952471	0.93[ASN][1000 genomes]
rs952472	0.93[ASN][1000 genomes]
rs965480	0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4886862	HMG20A	cis	cerebellum	SCAN
rs4886862	HEXA	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77627400-77657400	Weak transcription	Aorta	Aorta
2	chr15:77628200-77655400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:77628200-77655600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:77632200-77654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:77635000-77655400	Weak transcription	HSMM	muscle
6	chr15:77635000-77657400	Weak transcription	Fetal Intestine Large	intestine
7	chr15:77635200-77655600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:77636800-77658400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:77637200-77666800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:77639200-77659000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:77639600-77655600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:77639600-77657800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:77639600-77658800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:77639600-77664400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:77639800-77656800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:77639800-77657200	Weak transcription	Dnd41	blood
17	chr15:77639800-77657800	Weak transcription	Small Intestine	intestine
18	chr15:77639800-77687000	Weak transcription	Primary B cells from cord blood	blood
19	chr15:77640400-77662200	Weak transcription	HepG2	liver
20	chr15:77641000-77653600	Weak transcription	HUVEC	blood vessel
21	chr15:77641200-77652800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:77642600-77664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:77642600-77664800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:77642800-77657800	Weak transcription	Lung	lung
25	chr15:77644000-77658000	Weak transcription	Spleen	Spleen
26	chr15:77645600-77653400	Weak transcription	Fetal Lung	lung
27	chr15:77645600-77656600	Weak transcription	HSMMtube	muscle
28	chr15:77645800-77655400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:77645800-77655600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:77645800-77655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:77645800-77655800	Weak transcription	Placenta	Placenta
32	chr15:77645800-77662800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:77645800-77664200	Weak transcription	Brain Anterior Caudate	brain
34	chr15:77645800-77665800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:77645800-77665800	Weak transcription	Pancreas	Pancrea
36	chr15:77645800-77674000	Weak transcription	Ovary	ovary
37	chr15:77645800-77677000	Weak transcription	Right Ventricle	heart
38	chr15:77646000-77655600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:77646600-77661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:77646600-77661400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr15:77646800-77655800	Weak transcription	Adipose Nuclei	Adipose
42	chr15:77646800-77666000	Weak transcription	Stomach Mucosa	stomach
43	chr15:77647000-77655600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:77647000-77655600	Weak transcription	NHDF-Ad	bronchial
45	chr15:77647000-77657600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:77647000-77687200	Weak transcription	A549	lung
47	chr15:77648600-77685800	Weak transcription	Gastric	stomach
48	chr15:77649800-77653400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:77649800-77655600	Weak transcription	Fetal Stomach	stomach
50	chr15:77649800-77661200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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