Variant report

Variant	rs6492964
Chromosome Location	chr15:41053250-41053251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41047499..41049695-chr15:41052688..41055612,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10152546	0.84[CEU][hapmap]
rs10518697	0.85[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs1058734	0.85[CEU][hapmap]
rs11070283	0.85[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs12148915	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12442560	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12591044	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12592524	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12903817	0.84[CEU][hapmap]
rs12913739	0.85[CEU][hapmap]
rs12915171	0.87[CEU][hapmap]
rs17674454	0.85[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs17747633	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs1801321	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2619682	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34305357	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924486	0.85[CEU][hapmap]
rs4924492	0.84[AMR][1000 genomes]
rs4924496	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4924502	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5030789	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59244061	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7165509	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs7175905	0.83[EUR][1000 genomes]
rs7176245	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176590	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177265	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7180135	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7182499	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs957603	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv977702	chr15:41052749-41053346	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs6492964	RP11-111A22.1	cis	lung	GTEx
rs6492964	CCDC32	cis	multi-tissue	Pritchard
rs6492964	C15orf57	cis	Artery Tibial	GTEx
rs6492964	C15orf57	cis	brain	BrainEAC
rs6492964	MAPKBP1	cis	cerebellum	SCAN
rs6492964	C15orf57	cis	Nerve Tibial	GTEx
rs6492964	C15orf57	cis	Artery Aorta	GTEx
rs6492964	ZFYVE19	cis	cerebellum	SCAN
rs6492964	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs6492964	C15orf57	cis	lung	GTEx
rs6492964	C15orf57	cis	parietal	SCAN
rs6492964	SPINT1	cis	multi-tissue	Pritchard
rs6492964	C15orf57	cis	Heart Left Ventricle	GTEx
rs6492964	RAD51	cis	multi-tissue	Pritchard
rs6492964	RP11-111A22.1	cis	Artery Tibial	GTEx
rs6492964	C15orf57	cis	Muscle Skeletal	GTEx
rs6492964	CCDC32	cis	normal skin	skin_eQTL
rs6492964	C15orf57	cis	cerebellum	SCAN
rs6492964	MRPL42P5	cis	multi-tissue	Pritchard
rs6492964	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs6492964	C15orf57	cis	Esophagus Muscularis	GTEx
rs6492964	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs6492964	C15orf57	cis	Stomach	GTEx
rs6492964	C15orf57	cis	Esophagus Mucosa	GTEx
rs6492964	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41048000-41055000	Weak transcription	Pancreas	Pancrea
2	chr15:41048000-41055200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:41048000-41055200	Weak transcription	Brain Substantia Nigra	brain
4	chr15:41048000-41055200	Weak transcription	NH-A	brain
5	chr15:41048000-41055400	Weak transcription	Brain Angular Gyrus	brain
6	chr15:41048000-41055400	Weak transcription	Right Atrium	heart
7	chr15:41048200-41054600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:41048200-41055200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:41048200-41055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:41048200-41055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:41048200-41055400	Weak transcription	Liver	Liver
12	chr15:41048200-41055400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:41048200-41055400	Weak transcription	A549	lung
14	chr15:41048400-41055000	Weak transcription	Lung	lung
15	chr15:41048400-41055000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:41048400-41055200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:41048400-41055400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:41049200-41055200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:41049200-41055400	Weak transcription	GM12878-XiMat	blood
20	chr15:41049400-41054400	Weak transcription	Fetal Intestine Small	intestine
21	chr15:41049400-41054800	Weak transcription	Hela-S3	cervix
22	chr15:41049800-41054400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:41049800-41054600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41049800-41054600	Weak transcription	Fetal Intestine Large	intestine
25	chr15:41049800-41054800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:41049800-41055400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:41050600-41054800	Weak transcription	K562	blood
28	chr15:41052800-41054400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:41053000-41053400	Enhancers	HepG2	liver
30	chr15:41053000-41055000	Weak transcription	Fetal Thymus	thymus
31	chr15:41053000-41055600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:41053200-41055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:41053200-41055400	Weak transcription	Thymus	Thymus

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