Variant report

Variant	rs10782162
Chromosome Location	chr6:109806263-109806264
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109802624..109804740-chr6:109806103..109808684,3	MCF-7	breast:
2	chr6:109804505..109806373-chr6:109808766..109811459,2	K562	blood:
3	chr6:109702597..109705942-chr6:109803330..109806291,3	K562	blood:
4	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
5	chr6:109700978..109703685-chr6:109804896..109807033,2	MCF-7	breast:
6	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:

Variant related genes	Relation type
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000223537	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10080429	0.82[EUR][1000 genomes]
rs1040284	0.83[EUR][1000 genomes]
rs10457190	0.82[EUR][1000 genomes]
rs10457192	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs10457194	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs10457195	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1048203	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10499052	0.80[CEU][hapmap]
rs10499053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782161	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10782163	0.94[ASN][1000 genomes]
rs10872034	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153171	0.82[CEU][hapmap]
rs11153174	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs11153175	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs11153176	0.83[EUR][1000 genomes]
rs11153177	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153180	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153181	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153183	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs11153188	0.89[ASN][1000 genomes]
rs11752791	0.88[ASN][1000 genomes]
rs11753645	0.89[CEU][hapmap]
rs11754340	0.85[ASN][1000 genomes]
rs11754455	0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11755641	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.86[ASN][1000 genomes]
rs11967108	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs12190920	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190996	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12191353	0.81[ASN][1000 genomes]
rs12192776	0.82[ASN][1000 genomes]
rs12192847	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193493	0.83[EUR][1000 genomes]
rs12193719	0.86[ASN][1000 genomes]
rs12194061	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12194157	0.82[ASN][1000 genomes]
rs12197114	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12197180	0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs12197950	0.82[ASN][1000 genomes]
rs12198938	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs12199154	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs12205485	0.85[ASN][1000 genomes]
rs12206928	0.81[EUR][1000 genomes]
rs12208018	0.85[ASN][1000 genomes]
rs12208933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209691	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212476	0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs12213313	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12214639	0.86[ASN][1000 genomes]
rs12524273	0.84[EUR][1000 genomes]
rs12524502	0.85[CEU][hapmap]
rs12524639	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12528712	0.90[CEU][hapmap];0.93[MKK][hapmap]
rs12528781	0.85[ASN][1000 genomes]
rs12528822	0.95[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs12529505	0.80[CEU][hapmap]
rs13191066	0.85[ASN][1000 genomes]
rs13195517	0.90[CEU][hapmap]
rs13199135	0.86[ASN][1000 genomes]
rs13199519	0.90[CEU][hapmap]
rs13201947	0.88[ASN][1000 genomes]
rs13201951	0.91[ASN][1000 genomes]
rs13203252	0.89[CEU][hapmap]
rs13203587	0.95[ASN][1000 genomes]
rs13204102	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13204500	0.86[ASN][1000 genomes]
rs13204787	0.80[CEU][hapmap]
rs13212766	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1321328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs13220304	0.80[CEU][hapmap];0.81[MKK][hapmap]
rs13220915	0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1322816	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1358997	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1358998	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1406899	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs1476388	0.94[ASN][1000 genomes]
rs1546980	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1590306	0.83[EUR][1000 genomes]
rs17070580	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs1923725	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1960325	0.86[ASN][1000 genomes]
rs1980591	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1998811	0.95[ASN][1000 genomes]
rs2024849	0.95[ASN][1000 genomes]
rs2024850	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs2024852	0.95[ASN][1000 genomes]
rs2024853	0.86[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs2148089	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2208209	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236582	0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2275650	0.95[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2277114	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs2357124	0.88[ASN][1000 genomes]
rs34202013	0.82[EUR][1000 genomes]
rs35056702	0.82[EUR][1000 genomes]
rs36035949	0.84[EUR][1000 genomes]
rs36099706	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3757234	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3778475	0.83[EUR][1000 genomes]
rs3778477	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799835	0.90[CEU][hapmap]
rs3799839	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3807005	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818934	0.82[EUR][1000 genomes]
rs3899233	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap]
rs4490694	0.86[ASN][1000 genomes]
rs4945833	0.86[ASN][1000 genomes]
rs59056467	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59906308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68042406	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906216	0.93[ASN][1000 genomes]
rs6911700	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs6911838	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs6914498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6916579	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6920292	0.84[ASN][1000 genomes]
rs6920962	0.82[CEU][hapmap]
rs6926096	0.93[ASN][1000 genomes]
rs6929023	0.84[EUR][1000 genomes]
rs729888	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.82[ASN][1000 genomes]
rs7372	0.83[EUR][1000 genomes]
rs749517	0.94[ASN][1000 genomes]
rs752262	0.80[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7755941	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs7773095	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7773950	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs9320287	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs9480948	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9480951	0.82[EUR][1000 genomes]
rs9480953	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9480955	0.82[EUR][1000 genomes]
rs9480957	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9487068	0.81[EUR][1000 genomes]
rs9487094	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs9487095	0.82[EUR][1000 genomes]
rs9487100	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs971434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9885646	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10782162	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs10782162	SMPD2	cis	parietal	SCAN
rs10782162	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs10782162	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs10782162	SMPD2	cis	cerebellum	SCAN
rs10782162	AKD1	cis	cerebellum	SCAN
rs10782162	PPIL6	cis	cerebellum	SCAN
rs10782162	PDSS2	cis	cerebellum	SCAN
rs10782162	CD164	cis	parietal	SCAN
rs10782162	SMPD2	cis	Whole Blood	GTEx
rs10782162	MICAL1	cis	parietal	SCAN
rs10782162	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109804400-109814200	Weak transcription	Gastric	stomach
2	chr6:109805000-109806600	Weak transcription	Lung	lung
3	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:109805200-109806800	Enhancers	Fetal Muscle Leg	muscle
5	chr6:109805200-109806800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr6:109805200-109809200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:109805400-109806600	Weak transcription	Fetal Brain Female	brain
8	chr6:109805400-109807200	Weak transcription	A549	lung
9	chr6:109805400-109807200	Weak transcription	Hela-S3	cervix
10	chr6:109805400-109807400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:109805400-109807800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:109805400-109808800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:109805400-109812000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:109805600-109807000	Weak transcription	Stomach Mucosa	stomach
15	chr6:109805600-109807400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:109805600-109812400	Weak transcription	Brain Angular Gyrus	brain
17	chr6:109805800-109807000	Weak transcription	Placenta	Placenta
18	chr6:109806000-109806400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:109806000-109811400	Weak transcription	Dnd41	blood
20	chr6:109806200-109812200	Weak transcription	Primary hematopoietic stem cells	blood

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