Variant report

Variant	rs1127796
Chromosome Location	chr15:75193004-75193005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75192984-75193034	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:75192377-75193079	Raji	blood:	n/a	n/a
3	POLR2A	chr15:75192144-75193185	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr15:75191960-75193280	HCT-116	colon:	n/a	n/a
6	POLR2A	chr15:75192997-75193266	K562	blood:	n/a	n/a
7	POLR2A	chr15:75191924-75193436	U87	brain:	n/a	n/a
8	POLR2A	chr15:75192768-75193107	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75192708-75193342	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr15:75191083-75193522	HepG2	liver:	n/a	n/a
11	POLR2A	chr15:75192344-75193177	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:75192817-75193290	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:75192400-75193129	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr15:75192196-75193527	GM12891	blood:	n/a	n/a
15	POLR2A	chr15:75191618-75193452	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr15:75188926-75194641	U87	brain:	n/a	n/a
17	POLR2A	chr15:75191051-75193164	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr15:75192137-75193430	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:75192275-75193283	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:75192283-75194573	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:75192043-75193441	HCT-116	colon:	n/a	n/a
22	POLR2A	chr15:75192215-75193282	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr15:75188926-75193508	U87	brain:	n/a	n/a
24	POLR2A	chr15:75191042-75193090	GM12892	blood:	n/a	n/a
25	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr15:75192192-75193350	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr15:75187279-75194196	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:75191166-75193177	K562	blood:	n/a	n/a
29	POLR2A	chr15:75192591-75193009	A549	lung:	n/a	n/a
30	POLR2A	chr15:75191137-75195522	K562	blood:	n/a	n/a
31	POLR2A	chr15:75192408-75193044	GM12891	blood:	n/a	n/a
32	POLR2A	chr15:75192145-75193436	U87	brain:	n/a	n/a
33	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr15:75192233-75193146	HEK293	kidney:	n/a	n/a
35	POLR2A	chr15:75192276-75193482	K562	blood:	n/a	n/a
36	POLR2A	chr15:75191144-75194333	K562	blood:	n/a	n/a
37	POLR2A	chr15:75188556-75193697	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr15:75192296-75195541	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:75192393-75193172	K562	blood:	n/a	n/a
40	POLR2A	chr15:75192642-75193194	HepG2	liver:	n/a	n/a
41	POLR2A	chr15:75192440-75193291	MCF-7	breast:	n/a	n/a
42	POLR2A	chr15:75192325-75193265	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:75192232-75193306	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr15:75192570-75193264	HL-60	blood:	n/a	n/a
45	POLR2A	chr15:75188034-75193326	PFSK-1	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
2	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
3	chr15:75132595..75137581-chr15:75190842..75194074,4	K562	blood:
4	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
5	chr15:75152181..75153683-chr15:75192918..75194576,2	K562	blood:
6	chr15:75135336..75137971-chr15:75192308..75194100,2	MCF-7	breast:
7	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
8	chr15:75144129..75146019-chr15:75191068..75193901,2	MCF-7	breast:
9	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
10	chr15:75134794..75137581-chr15:75190842..75193156,3	K562	blood:
11	chr15:75074806..75076876-chr15:75192504..75194161,2	K562	blood:
12	chr15:75091765..75094357-chr15:75191183..75194158,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPI-1	chr15:75192825-75193030	ENSG00000260824.1

No data

Variant related genes	Relation type
FAM219B	TF binding region
ENSG00000103653	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11072511	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11072512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11072514	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1130741	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs1133322	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133323	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11630918	0.96[CEU][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633472	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11638130	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11639413	0.81[EUR][1000 genomes]
rs11854704	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856413	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857695	0.94[EUR][1000 genomes]
rs12487	0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap]
rs12898539	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899430	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12899787	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900662	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12901190	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12902515	0.94[EUR][1000 genomes]
rs12903205	0.95[EUR][1000 genomes]
rs12903370	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12904326	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12904897	0.96[EUR][1000 genomes]
rs12907898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908365	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909335	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12911254	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912839	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12913293	0.98[EUR][1000 genomes]
rs12914217	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1378942	1.00[LWK][hapmap]
rs16973078	1.00[YRI][hapmap]
rs2044157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2168518	1.00[LWK][hapmap]
rs2290573	1.00[LWK][hapmap];0.83[MKK][hapmap]
rs2415251	0.92[CEU][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs35556055	0.83[MEX][hapmap]
rs4643278	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886608	0.92[EUR][1000 genomes]
rs4886632	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886636	0.96[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4886639	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886640	0.80[EUR][1000 genomes]
rs59945415	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62029167	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495122	0.89[CEU][hapmap]
rs7495664	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7495739	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs7497026	0.94[EUR][1000 genomes]
rs7497393	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8025447	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1127796	CYP11A1	cis	cerebellum	SCAN
rs1127796	MPI	cis	multi-tissue	Pritchard
rs1127796	SCAMP2	cis	Esophagus Mucosa	GTEx
rs1127796	ETFA	cis	cerebellum	SCAN
rs1127796	TLE3	cis	cerebellum	SCAN
rs1127796	SCAMP2	cis	parietal	SCAN
rs1127796	ULK3	cis	multi-tissue	Pritchard
rs1127796	ULK3	cis	parietal	SCAN
rs1127796	ZNF572	trans	cerebellum	SCAN
rs1127796	SCAMP2	cis	Whole Blood	GTEx
rs1127796	MPI	cis	lymphoblastoid	seeQTL
rs1127796	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
4	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
6	chr15:75185000-75193800	Strong transcription	Fetal Intestine Small	intestine
7	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
8	chr15:75185200-75193800	Strong transcription	Fetal Intestine Large	intestine
9	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
10	chr15:75186200-75193600	Weak transcription	Stomach Mucosa	stomach
11	chr15:75186800-75195800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:75187200-75193400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:75187200-75193600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:75187400-75193600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:75187600-75193600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:75187600-75193800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:75187600-75197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:75187800-75193600	Strong transcription	Primary T cells from cord blood	blood
19	chr15:75187800-75193800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:75187800-75193800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:75187800-75194000	Strong transcription	A549	lung
22	chr15:75187800-75196600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:75187800-75196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:75187800-75197400	Strong transcription	Fetal Thymus	thymus
25	chr15:75188000-75193400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:75188000-75193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:75188000-75193600	Strong transcription	Liver	Liver
28	chr15:75188000-75193800	Strong transcription	Brain Hippocampus Middle	brain
29	chr15:75188000-75193800	Strong transcription	K562	blood
30	chr15:75188000-75196000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:75188000-75196800	Strong transcription	Brain Germinal Matrix	brain
32	chr15:75188000-75197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:75188000-75197000	Strong transcription	Fetal Brain Female	brain
34	chr15:75188000-75197600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:75188200-75193400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:75188200-75193800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:75188200-75193800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:75188200-75193800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:75188200-75195000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:75188200-75195600	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr15:75188200-75197400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:75188200-75197400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:75188200-75197600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:75188400-75193600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:75188400-75193800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr15:75188400-75193800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:75188400-75193800	Strong transcription	NHLF	lung
48	chr15:75188400-75196600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:75188400-75197400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:75188400-75197400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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