Variant report

Variant	rs12197114
Chromosome Location	chr6:109735498-109735499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109735393..109737458-chr6:109775192..109778139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135596	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10080429	0.95[EUR][1000 genomes]
rs1040284	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457190	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10457194	0.86[CHB][hapmap]
rs10457195	0.86[CHB][hapmap]
rs1048203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782161	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782162	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10872032	0.92[EUR][1000 genomes]
rs10872034	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153171	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11153174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153176	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap]
rs11753645	0.81[CEU][hapmap]
rs11754455	0.86[CHB][hapmap]
rs11755641	0.86[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12190920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190996	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192847	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193493	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197180	0.86[CHB][hapmap]
rs12198938	0.86[CHB][hapmap]
rs12199154	0.86[CHB][hapmap]
rs12206928	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12208933	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12209691	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap]
rs12213313	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524273	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528712	0.85[CEU][hapmap]
rs12528822	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220915	0.86[CHB][hapmap]
rs1322816	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358997	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap]
rs1546980	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1590306	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024850	0.86[CHB][hapmap]
rs2236582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap]
rs34202013	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35056702	0.95[EUR][1000 genomes]
rs36035949	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36099706	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778475	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778477	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799835	0.82[CEU][hapmap]
rs3799839	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807005	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818934	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59056467	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59906308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68042406	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911838	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6914498	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs6920962	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6929023	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7372	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752262	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7754650	0.86[YRI][hapmap]
rs7755941	0.90[CHB][hapmap]
rs7773095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap]
rs9320287	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs9480933	0.91[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9480951	0.95[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs9480955	0.95[EUR][1000 genomes]
rs9480957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487068	0.94[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs9487095	0.95[EUR][1000 genomes]
rs9487097	0.91[EUR][1000 genomes]
rs9487098	0.92[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885646	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12197114	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12197114	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12197114	SMPD2	cis	multi-tissue	Pritchard
rs12197114	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12197114	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12197114	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
2	chr6:109706600-109735800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:109712800-109736200	Weak transcription	Left Ventricle	heart
5	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
6	chr6:109724400-109750400	Weak transcription	Ovary	ovary
7	chr6:109725000-109736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:109731400-109745200	Weak transcription	Pancreas	Pancrea
10	chr6:109735200-109750200	Weak transcription	Fetal Muscle Leg	muscle

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