Variant report

Variant	rs17236770
Chromosome Location	chr15:34517995-34517996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr15:34516152-34518004	A549	lung:	n/a	n/a
2	POLR2A	chr15:34516767-34518325	GM12878	blood:	n/a	n/a
3	MXI1	chr15:34515886-34518224	SK-N-SH	brain:	n/a	n/a
4	ESRRA	chr15:34516281-34518261	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:34517991-34518002	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:34517851-34518424	GM12878	blood:	n/a	n/a
7	HCFC1	chr15:34516869-34518061	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:34391770..34396248-chr15:34515474..34518631,5	K562	blood:
2	chr15:34392855..34396101-chr15:34515904..34518783,5	MCF-7	breast:
3	chr15:34516456..34519073-chr15:34530589..34533176,2	MCF-7	breast:
4	chr15:34515761..34518007-chr15:34659442..34662221,3	K562	blood:
5	chr15:34393239..34395470-chr15:34515986..34518807,4	MCF-7	breast:
6	chr15:34515223..34518649-chr15:34658701..34662221,4	K562	blood:
7	chr15:34516218..34520145-chr15:34531781..34533965,3	K562	blood:
8	chr15:34498121..34503791-chr15:34514506..34519551,14	K562	blood:
9	chr15:34515788..34518726-chr15:34518893..34520736,3	K562	blood:
10	chr15:34517046..34518726-chr15:34519236..34520864,2	K562	blood:
11	chr15:34516899..34519877-chr15:34627913..34631706,5	K562	blood:
12	chr15:34516899..34519877-chr15:34629611..34631706,2	K562	blood:
13	chr15:34497680..34504001-chr15:34514973..34521212,14	K562	blood:
14	chr15:34515594..34518445-chr15:34530011..34531536,2	K562	blood:
15	chr15:34516970..34518662-chr15:34536000..34538660,2	K562	blood:

No data

Variant related genes	Relation type
EMC4	TF binding region
ENSG00000182405	Chromatin interaction
ENSG00000176454	Chromatin interaction
ENSG00000134152	Chromatin interaction
ENSG00000128463	Chromatin interaction
ENSG00000134153	Chromatin interaction
ENSG00000140199	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10519916	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11638909	0.81[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12438953	0.96[EUR][1000 genomes]
rs16958873	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16958875	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17236749	0.86[MEX][hapmap]
rs17817770	0.86[MEX][hapmap]
rs2169480	1.00[ASW][hapmap]
rs3764236	0.86[MEX][hapmap]
rs3794518	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4779660	1.00[GIH][hapmap]
rs7161944	0.86[MEX][hapmap]
rs73386041	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74010034	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74010036	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028501	0.81[CEU][hapmap]
rs8033087	0.97[EUR][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	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17236770	HERC2	cis	parietal	SCAN
rs17236770	APBA2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34516000-34518200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:34516000-34518200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:34516000-34518400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:34516000-34518400	Active TSS	Fetal Intestine Small	intestine
5	chr15:34516000-34518400	Active TSS	A549	lung
6	chr15:34516000-34518400	Active TSS	K562	blood
7	chr15:34516200-34518000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:34516200-34518000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr15:34516200-34518000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:34516200-34518000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:34516200-34518000	Active TSS	Esophagus	oesophagus
12	chr15:34516200-34518000	Active TSS	Fetal Kidney	kidney
13	chr15:34516200-34518000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr15:34516200-34518000	Active TSS	HSMMtube	muscle
15	chr15:34516200-34518200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr15:34516200-34518200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:34516200-34518200	Active TSS	Psoas Muscle	Psoas
18	chr15:34516200-34518200	Active TSS	Right Atrium	heart
19	chr15:34516200-34518200	Active TSS	NHLF	lung
20	chr15:34516200-34518400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:34516200-34518400	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:34516200-34518400	Active TSS	HSMM	muscle
23	chr15:34516200-34518600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr15:34516400-34518000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:34516400-34518000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:34516400-34518000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr15:34516400-34518000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:34516400-34518000	Active TSS	Ovary	ovary
29	chr15:34516400-34518000	Bivalent/Poised TSS	HepG2	liver
30	chr15:34516400-34518400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr15:34516400-34518400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:34516600-34518000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:34516600-34518000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:34516600-34518000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:34516600-34518000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:34516600-34518000	Active TSS	Fetal Brain Male	brain
37	chr15:34516600-34518000	Active TSS	Pancreas	Pancrea
38	chr15:34516600-34518000	Active TSS	NHDF-Ad	bronchial
39	chr15:34516600-34518200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:34516600-34518200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:34516600-34518200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:34516600-34518200	Active TSS	Rectal Smooth Muscle	rectum
43	chr15:34516800-34518000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:34516800-34518000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr15:34516800-34518000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:34517000-34518200	Active TSS	Fetal Muscle Trunk	muscle
47	chr15:34517200-34518000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:34517200-34518200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:34517200-34518200	Transcr. at gene 5' and 3'	Fetal Lung	lung
50	chr15:34517400-34518000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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