Variant report

Variant	rs752262
Chromosome Location	chr6:109770999-109771000
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109770860-109771213	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:109769023-109772168	GM19099	blood:	n/a	n/a
3	POLR2A	chr6:109770411-109771551	GM18951	blood:	n/a	n/a
4	POLR2A	chr6:109767323-109771840	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:109766660-109772354	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr6:109767219-109772309	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:109770411-109771582	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:109770295-109771047	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr6:109767216-109772257	GM18505	blood:	n/a	n/a
10	POLR2A	chr6:109767128-109772358	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:109768107-109771902	GM19193	blood:	n/a	n/a
12	MTA3	chr6:109770095-109771612	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:109769104-109771786	MCF-7	breast:	n/a	n/a
14	POLR2A	chr6:109765770-109771599	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:109767429-109772368	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr6:109770256-109771624	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:109768290-109771209	MCF-7	breast:	n/a	n/a
18	POLR2A	chr6:109768010-109771572	K562	blood:	n/a	n/a
19	POLR2A	chr6:109765681-109771914	GM12892	blood:	n/a	n/a
20	POLR2A	chr6:109770939-109771263	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:109765710-109771793	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:109770308-109771524	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:109767133-109771962	K562	blood:	n/a	n/a
24	POLR2A	chr6:109770881-109771542	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:109769585-109771084	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:109763209-109771395	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr6:109770279-109771933	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:109770767-109771374	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr6:109767054-109771924	K562	blood:	n/a	n/a
30	POLR2A	chr6:109761500-109772072	GM12892	blood:	n/a	n/a
31	POLR2A	chr6:109770320-109771043	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:109766420-109772338	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr6:109767945-109771836	A549	lung:	n/a	n/a
34	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
36	POLR2A	chr6:109763255-109772269	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:48610607..48612431-chr6:109769391..109772188,2	MCF-7	breast:
2	chr6:109770371..109773024-chr6:109807786..109809712,3	MCF-7	breast:

No data

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000049283	Chromatin interaction
ENSG00000223537	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10080429	0.89[EUR][1000 genomes]
rs1040284	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10457190	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10457192	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs10457194	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs10457195	0.86[CHB][hapmap]
rs1048203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10782161	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782162	0.80[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782163	0.82[ASN][1000 genomes]
rs10872032	0.86[EUR][1000 genomes]
rs10872034	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153171	0.82[JPT][hapmap]
rs11153174	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153175	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153176	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11153177	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11153180	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11153181	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs11754455	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs11755641	0.86[CHB][hapmap]
rs11967108	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190920	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190996	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192847	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12193493	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197114	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12197180	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12198938	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs12199154	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs12206928	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12208933	0.81[CHB][hapmap]
rs12209691	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs12213313	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524273	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12524639	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12528822	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13201951	0.80[ASN][1000 genomes]
rs13203587	0.83[ASN][1000 genomes]
rs13212766	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13220915	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs1322816	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1358997	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1358998	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs1476388	0.82[ASN][1000 genomes]
rs1546980	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590306	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17070580	0.89[EUR][1000 genomes]
rs1923725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1980591	0.85[CHB][hapmap]
rs1998811	0.83[ASN][1000 genomes]
rs2024849	0.83[ASN][1000 genomes]
rs2024850	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2024852	0.83[ASN][1000 genomes]
rs2024853	0.83[ASN][1000 genomes]
rs2236582	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275650	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs34202013	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35056702	0.89[EUR][1000 genomes]
rs36035949	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36099706	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3778475	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778477	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799839	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3807005	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818934	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59056467	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59906308	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68042406	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6906216	0.80[ASN][1000 genomes]
rs6911838	0.90[EUR][1000 genomes]
rs6914498	0.81[CHB][hapmap]
rs6916579	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926096	0.80[ASN][1000 genomes]
rs6929023	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs729888	0.86[CHB][hapmap]
rs7372	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749517	0.82[ASN][1000 genomes]
rs7755941	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs7773095	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs9320287	0.89[EUR][1000 genomes]
rs9480933	0.85[EUR][1000 genomes]
rs9480948	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9480951	0.89[EUR][1000 genomes]
rs9480953	0.89[EUR][1000 genomes]
rs9480955	0.89[EUR][1000 genomes]
rs9480957	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9487068	0.88[EUR][1000 genomes]
rs9487094	0.89[EUR][1000 genomes]
rs9487095	0.89[EUR][1000 genomes]
rs9487097	0.86[EUR][1000 genomes]
rs9487098	0.86[EUR][1000 genomes]
rs9487100	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9885646	0.89[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs752262	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs752262	SMPD2	cis	Whole Blood	GTEx
rs752262	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs752262	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs752262	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
4	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
5	chr6:109763400-109775000	Strong transcription	NHLF	lung
6	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:109763600-109773200	Weak transcription	Fetal Brain Male	brain
8	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
11	chr6:109763800-109771000	Strong transcription	Fetal Intestine Small	intestine
12	chr6:109763800-109774400	Strong transcription	HSMM	muscle
13	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
15	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
16	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:109763800-109775600	Weak transcription	HepG2	liver
19	chr6:109764000-109774400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr6:109764000-109774600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:109764000-109774800	Strong transcription	Fetal Intestine Large	intestine
22	chr6:109764000-109775000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:109764200-109774600	Strong transcription	Brain Germinal Matrix	brain
24	chr6:109764200-109774600	Weak transcription	Stomach Mucosa	stomach
25	chr6:109764200-109774800	Strong transcription	Fetal Brain Female	brain
26	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
27	chr6:109765000-109771800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:109765400-109773600	Strong transcription	NHDF-Ad	bronchial
29	chr6:109765400-109773800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:109766800-109773200	Weak transcription	NH-A	brain
32	chr6:109766800-109775200	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:109767000-109776000	Weak transcription	A549	lung
35	chr6:109767200-109776000	Weak transcription	Osteobl	bone
36	chr6:109767400-109774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:109767800-109773000	Weak transcription	HMEC	breast
38	chr6:109768000-109772200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:109768000-109772800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:109768200-109772600	Weak transcription	Fetal Lung	lung
41	chr6:109768200-109772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:109768200-109774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:109768400-109771000	Weak transcription	Dnd41	blood
44	chr6:109768400-109771200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:109768400-109771800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:109768400-109772000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:109768400-109772800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:109768400-109772800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:109768400-109773000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:109768400-109775800	Weak transcription	Liver	Liver

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