Variant report

Variant	rs7495739
Chromosome Location	chr15:75185670-75185671
allele	A/G
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:7)
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	SPI1	chr15:75185091-75185845	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75184699-75185892	K562	blood:	n/a	n/a
3	SPI1	chr15:75185273-75185699	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:75184693-75186288	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:75184303-75187131	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:75184526-75186376	SK-N-MC	brain:	n/a	n/a
7	CTCF	chr15:75185520-75185670	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75142292..75144361-chr15:75184873..75186770,2	K562	blood:
2	chr15:75130141..75132356-chr15:75184160..75186177,2	K562	blood:
3	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
4	chr15:75109719..75111456-chr15:75185022..75186522,2	MCF-7	breast:
5	chr15:75072512..75079183-chr15:75180576..75186728,11	MCF-7	breast:
6	chr15:75144564..75147431-chr15:75184643..75187545,2	MCF-7	breast:
7	chr15:75184495..75186934-chr15:75223439..75225977,2	K562	blood:

No data

Variant related genes	Relation type
MPI	TF binding region
ENSG00000103653	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11072511	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072512	1.00[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs11072513	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11072514	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1127796	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs1130741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133322	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1133323	0.96[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11630918	0.96[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11633472	1.00[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs11638130	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs11639413	0.80[EUR][1000 genomes]
rs11854704	0.96[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs11856413	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs11857695	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439641	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs12441499	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs12487	0.92[CEU][hapmap]
rs12898539	0.88[EUR][1000 genomes]
rs12899430	0.88[EUR][1000 genomes]
rs12899787	0.93[EUR][1000 genomes]
rs12900662	0.93[EUR][1000 genomes]
rs12901190	0.96[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12902515	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903205	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12903370	0.86[EUR][1000 genomes]
rs12904326	0.86[EUR][1000 genomes]
rs12904897	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907898	0.96[EUR][1000 genomes]
rs12908365	0.94[EUR][1000 genomes]
rs12909335	0.96[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12911254	0.86[EUR][1000 genomes]
rs12912839	0.86[EUR][1000 genomes]
rs12913293	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914217	0.85[EUR][1000 genomes]
rs2044157	0.84[EUR][1000 genomes]
rs2415251	0.92[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs3935818	0.95[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4643278	0.93[EUR][1000 genomes]
rs4886608	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886632	0.97[EUR][1000 genomes]
rs4886636	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886639	0.87[EUR][1000 genomes]
rs4886640	0.80[AFR][1000 genomes]
rs56671860	0.86[AFR][1000 genomes]
rs59945415	0.93[EUR][1000 genomes]
rs60494786	0.86[AFR][1000 genomes]
rs62029167	0.94[EUR][1000 genomes]
rs6495122	0.89[CEU][hapmap]
rs6495128	0.80[ASN][1000 genomes]
rs6495129	0.80[ASN][1000 genomes]
rs7179093	0.95[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs729263	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs7495664	0.87[EUR][1000 genomes]
rs7497026	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7497393	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8025447	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032473	0.82[AFR][1000 genomes]
rs9672491	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription 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	55 gene(s)	inside rSNPs	diseases
2	esv990390	chr15:75179300-75187945	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7495739	ULK3	cis	multi-tissue	Pritchard
rs7495739	ULK3	cis	Whole Blood	GTEx
rs7495739	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs7495739	SCAMP2	cis	Whole Blood	GTEx
rs7495739	SCAMP2	cis	parietal	SCAN
rs7495739	CYP11A1	cis	cerebellum	SCAN
rs7495739	ZNF572	trans	cerebellum	SCAN
rs7495739	TLE3	cis	cerebellum	SCAN
rs7495739	SCAMP2	cis	Esophagus Mucosa	GTEx
rs7495739	ETFA	cis	cerebellum	SCAN
rs7495739	SCAMP5	cis	Artery Tibial	GTEx
rs7495739	ULK3	cis	parietal	SCAN
rs7495739	MPI	cis	multi-tissue	Pritchard
rs7495739	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs7495739	MPI	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75185800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:75183200-75186200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr15:75183200-75189400	Weak transcription	Psoas Muscle	Psoas
4	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
6	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
7	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:75183400-75185800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:75183400-75186000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr15:75183400-75186200	Genic enhancers	Esophagus	oesophagus
11	chr15:75183400-75186200	Genic enhancers	Pancreas	Pancrea
12	chr15:75183400-75186200	Strong transcription	Osteobl	bone
13	chr15:75183400-75186400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:75183400-75186400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:75183400-75186400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:75183400-75186400	Genic enhancers	NHEK	skin
17	chr15:75183400-75192200	Weak transcription	NH-A	brain
18	chr15:75183600-75185800	Genic enhancers	GM12878-XiMat	blood
19	chr15:75183600-75186000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr15:75183600-75186200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:75183600-75186200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:75183600-75186200	Strong transcription	Brain Hippocampus Middle	brain
23	chr15:75183600-75186200	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr15:75183600-75186200	Strong transcription	Fetal Lung	lung
25	chr15:75183600-75186200	Strong transcription	NHDF-Ad	bronchial
26	chr15:75183600-75186200	Strong transcription	NHLF	lung
27	chr15:75183600-75186400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:75183600-75186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:75183600-75186400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:75183600-75186400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:75183600-75186400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:75183600-75186400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:75183600-75187200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
36	chr15:75183800-75185800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:75183800-75185800	Strong transcription	Aorta	Aorta
38	chr15:75183800-75185800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr15:75183800-75186000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:75183800-75186000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:75183800-75186000	Strong transcription	Brain Angular Gyrus	brain
42	chr15:75183800-75186000	Strong transcription	Fetal Brain Female	brain
43	chr15:75183800-75186000	Strong transcription	Fetal Thymus	thymus
44	chr15:75183800-75186000	Genic enhancers	Gastric	stomach
45	chr15:75183800-75186000	Strong transcription	Ovary	ovary
46	chr15:75183800-75186200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr15:75183800-75186200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75183800-75186200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr15:75183800-75186200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:75183800-75186200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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