Variant report

Variant	rs10872034
Chromosome Location	chr6:109807239-109807240
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr6:109807235-109807602	A549	lung:	n/a	n/a
2	STAT3	chr6:109806755-109807852	MCF10A-Er-Src	breast:	n/a	chr6:109807524-109807535

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109802624..109804740-chr6:109806103..109808684,3	MCF-7	breast:

Variant related genes	Relation type
ZBTB24	TF binding region
ENSG00000223537	TF binding region
ENSG00000112365	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10080429	0.82[EUR][1000 genomes]
rs1040284	0.83[EUR][1000 genomes]
rs10457190	0.82[EUR][1000 genomes]
rs10457192	0.95[ASN][1000 genomes]
rs10457194	0.92[ASN][1000 genomes]
rs10457195	0.90[ASN][1000 genomes]
rs1048203	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10499053	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782161	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10782162	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782163	0.94[ASN][1000 genomes]
rs11153174	0.83[EUR][1000 genomes]
rs11153175	0.83[EUR][1000 genomes]
rs11153176	0.83[EUR][1000 genomes]
rs11153177	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153180	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153181	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153183	0.95[ASN][1000 genomes]
rs11153188	0.89[ASN][1000 genomes]
rs11752791	0.88[ASN][1000 genomes]
rs11754340	0.85[ASN][1000 genomes]
rs11754455	0.95[ASN][1000 genomes]
rs11755641	0.86[ASN][1000 genomes]
rs11967108	0.83[EUR][1000 genomes]
rs12190920	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190996	0.90[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	0.90[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	0.89[ASN][1000 genomes]
rs12194157	0.82[ASN][1000 genomes]
rs12197114	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12197180	0.93[ASN][1000 genomes]
rs12197950	0.82[ASN][1000 genomes]
rs12198938	0.95[ASN][1000 genomes]
rs12199154	0.95[ASN][1000 genomes]
rs12205485	0.85[ASN][1000 genomes]
rs12206928	0.81[EUR][1000 genomes]
rs12208018	0.85[ASN][1000 genomes]
rs12208933	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209691	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212476	0.95[ASN][1000 genomes]
rs12213313	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12214639	0.86[ASN][1000 genomes]
rs12524273	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12524639	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12528781	0.85[ASN][1000 genomes]
rs12528822	0.82[EUR][1000 genomes]
rs13191066	0.85[ASN][1000 genomes]
rs13199135	0.86[ASN][1000 genomes]
rs13201947	0.88[ASN][1000 genomes]
rs13201951	0.91[ASN][1000 genomes]
rs13203587	0.95[ASN][1000 genomes]
rs13204102	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13204500	0.86[ASN][1000 genomes]
rs13212766	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1321328	0.82[ASN][1000 genomes]
rs13220915	0.95[ASN][1000 genomes]
rs1322816	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1358997	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1358998	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1406899	0.95[ASN][1000 genomes]
rs1476388	0.94[ASN][1000 genomes]
rs1546980	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1590306	0.83[EUR][1000 genomes]
rs17070580	0.82[EUR][1000 genomes]
rs1923725	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1960325	0.86[ASN][1000 genomes]
rs1980591	0.85[ASN][1000 genomes]
rs1998811	0.95[ASN][1000 genomes]
rs2024849	0.95[ASN][1000 genomes]
rs2024850	0.95[ASN][1000 genomes]
rs2024852	0.95[ASN][1000 genomes]
rs2024853	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	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2275650	0.82[EUR][1000 genomes]
rs2277114	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	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3757234	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3778475	0.83[EUR][1000 genomes]
rs3778477	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799839	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3807005	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818934	0.82[EUR][1000 genomes]
rs4490694	0.86[ASN][1000 genomes]
rs4945833	0.86[ASN][1000 genomes]
rs59056467	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59906308	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68042406	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906216	0.93[ASN][1000 genomes]
rs6911838	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6914498	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6916579	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6920292	0.84[ASN][1000 genomes]
rs6926096	0.93[ASN][1000 genomes]
rs6929023	0.84[EUR][1000 genomes]
rs729888	0.82[ASN][1000 genomes]
rs7372	0.83[EUR][1000 genomes]
rs749517	0.94[ASN][1000 genomes]
rs752262	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7755941	0.95[ASN][1000 genomes]
rs7773095	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7773950	0.95[ASN][1000 genomes]
rs9320287	0.82[EUR][1000 genomes]
rs9480948	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9480951	0.82[EUR][1000 genomes]
rs9480953	0.82[EUR][1000 genomes]
rs9480955	0.82[EUR][1000 genomes]
rs9480957	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9487068	0.81[EUR][1000 genomes]
rs9487094	0.82[EUR][1000 genomes]
rs9487095	0.82[EUR][1000 genomes]
rs9487100	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs971434	0.82[ASN][1000 genomes]
rs9885646	0.82[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10872034	SMPD2	cis	Whole Blood	GTEx
rs10872034	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs10872034	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs10872034	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109804400-109814200	Weak transcription	Gastric	stomach
2	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:109805200-109809200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:109805400-109807400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:109805400-109807800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:109805400-109808800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:109805400-109812000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:109805600-109807400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:109805600-109812400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:109806000-109811400	Weak transcription	Dnd41	blood
11	chr6:109806200-109812200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:109806400-109807600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:109806800-109812200	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:109807000-109807400	Enhancers	Placenta	Placenta
15	chr6:109807200-109807400	Enhancers	Stomach Mucosa	stomach
16	chr6:109807200-109808000	Enhancers	Hela-S3	cervix

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