Variant report

Variant	rs1486877
Chromosome Location	chr15:59463832-59463833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59462457-59464212	A549	lung:	n/a	n/a
2	POLR2A	chr15:59463238-59463832	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:59463123-59463903	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
MIR2116	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10775168	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11071409	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11071410	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574500	1.00[ASN][1000 genomes]
rs11630246	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13498	1.00[ASN][1000 genomes]
rs16941077	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17269496	1.00[ASN][1000 genomes]
rs17269503	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1979552	1.00[ASN][1000 genomes]
rs2087123	0.83[CHD][hapmap]
rs28739025	1.00[ASN][1000 genomes]
rs4775121	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775122	0.90[YRI][hapmap]
rs57164516	1.00[ASN][1000 genomes]
rs60440107	1.00[ASN][1000 genomes]
rs61055592	1.00[ASN][1000 genomes]
rs6494072	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173787	1.00[ASN][1000 genomes]
rs7174992	1.00[ASN][1000 genomes]
rs7175697	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs74017367	1.00[ASN][1000 genomes]
rs8027376	1.00[CHD][hapmap]
rs8036093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041633	1.00[ASN][1000 genomes]
rs931346	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59431800-59467200	Weak transcription	Fetal Brain Female	brain
2	chr15:59432000-59465600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59434200-59467000	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
5	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
6	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
7	chr15:59445800-59467000	Weak transcription	Fetal Heart	heart
8	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
11	chr15:59451800-59464600	Weak transcription	Brain Angular Gyrus	brain
12	chr15:59451800-59466000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:59453400-59467200	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:59453800-59470000	Weak transcription	Right Ventricle	heart
15	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:59455200-59467200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:59458000-59470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:59459000-59464800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:59459200-59466800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr15:59459400-59467000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:59460200-59464000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:59460400-59464200	Enhancers	NHDF-Ad	bronchial
25	chr15:59460600-59464800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:59460600-59464800	Genic enhancers	NHEK	skin
27	chr15:59460600-59465800	Strong transcription	GM12878-XiMat	blood
28	chr15:59460800-59466200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:59461000-59474800	Strong transcription	Liver	Liver
30	chr15:59461200-59466200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:59461200-59467000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:59461400-59466800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:59461600-59466400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:59461800-59467200	Strong transcription	Hela-S3	cervix
35	chr15:59462000-59464200	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr15:59462000-59464600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:59462000-59465000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:59462000-59466800	Strong transcription	Fetal Intestine Small	intestine
39	chr15:59462000-59467000	Strong transcription	Fetal Intestine Large	intestine
40	chr15:59462000-59467200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr15:59462200-59464200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:59462400-59465400	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:59462400-59465400	Strong transcription	Fetal Stomach	stomach
44	chr15:59462400-59467200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:59462600-59464200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:59462600-59464200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr15:59462600-59464800	Genic enhancers	HMEC	breast
48	chr15:59462600-59466800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:59462800-59464400	Strong transcription	Lung	lung
50	chr15:59462800-59466200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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