Variant report

Variant	rs12190920
Chromosome Location	chr6:109800599-109800600
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109766673..109769201-chr6:109798430..109801986,3	MCF-7	breast:
2	chr6:109417075..109418905-chr6:109799494..109801799,2	K562	blood:
3	chr6:109702682..109704244-chr6:109798920..109800659,2	K562	blood:
4	chr6:109785634..109787468-chr6:109799694..109802286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000135596	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10080429	0.86[EUR][1000 genomes]
rs1040284	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457190	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10457192	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs10457194	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10457195	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs1048203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10499053	0.95[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10782161	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782162	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]
rs10782163	0.85[ASN][1000 genomes]
rs10872032	0.83[EUR][1000 genomes]
rs10872034	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153171	0.86[CEU][hapmap]
rs11153174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153176	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153177	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153180	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153181	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153183	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs11153188	0.81[ASN][1000 genomes]
rs11753645	0.80[CEU][hapmap]
rs11754455	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs11755641	0.90[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190996	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12192847	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193493	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194061	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs12197114	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]
rs12197180	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs12198938	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs12199154	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs12206928	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208933	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs12209691	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212476	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12213313	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524273	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12524639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12528712	0.85[CEU][hapmap]
rs12528822	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13201951	0.83[ASN][1000 genomes]
rs13203252	0.83[CEU][hapmap]
rs13203587	0.85[ASN][1000 genomes]
rs13212766	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321328	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs13220915	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1322816	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1358997	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1358998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1406899	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1476388	0.85[ASN][1000 genomes]
rs1546980	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590306	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980591	0.90[CHB][hapmap]
rs1998811	0.85[ASN][1000 genomes]
rs2024849	0.85[ASN][1000 genomes]
rs2024850	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2024852	0.85[ASN][1000 genomes]
rs2024853	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2208209	0.81[EUR][1000 genomes]
rs2236582	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275650	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277114	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs34202013	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35056702	0.87[EUR][1000 genomes]
rs36035949	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36099706	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778475	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778477	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799835	0.81[CEU][hapmap]
rs3799839	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3807005	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818934	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3899233	0.90[CHB][hapmap]
rs59056467	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59906308	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68042406	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906216	0.83[ASN][1000 genomes]
rs6911700	0.90[CHB][hapmap]
rs6911838	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6914498	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap]
rs6916579	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6920962	0.87[CEU][hapmap]
rs6926096	0.83[ASN][1000 genomes]
rs6929023	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs729888	0.90[CHB][hapmap]
rs7372	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749517	0.85[ASN][1000 genomes]
rs752262	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]
rs7755941	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7773095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7773950	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs9320287	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9480933	0.82[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480951	0.87[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9480955	0.87[EUR][1000 genomes]
rs9480957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487068	0.85[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9487095	0.87[EUR][1000 genomes]
rs9487097	0.83[EUR][1000 genomes]
rs9487098	0.83[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs971434	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs9885646	0.95[CEU][hapmap];0.87[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12190920	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12190920	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12190920	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12190920	SMPD2	cis	Whole Blood	GTEx
rs12190920	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109781400-109802200	Strong transcription	HSMM	muscle
2	chr6:109782400-109803000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:109787800-109800600	Weak transcription	Fetal Heart	heart
4	chr6:109789400-109803200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:109794400-109801200	Weak transcription	HSMMtube	muscle
6	chr6:109795200-109802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:109797800-109803400	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr6:109798000-109803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:109798000-109803400	Genic enhancers	Fetal Thymus	thymus
10	chr6:109798200-109802200	Weak transcription	Gastric	stomach
11	chr6:109798200-109803000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:109798600-109802600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:109798600-109802800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
14	chr6:109798600-109803400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr6:109798800-109800600	Enhancers	Brain Germinal Matrix	brain
16	chr6:109798800-109800800	Enhancers	Stomach Mucosa	stomach
17	chr6:109798800-109801200	Enhancers	Adipose Nuclei	Adipose
18	chr6:109798800-109801200	Enhancers	Small Intestine	intestine
19	chr6:109798800-109801600	Enhancers	Right Atrium	heart
20	chr6:109798800-109802400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
21	chr6:109799000-109800600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:109799000-109801800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:109799000-109801800	Weak transcription	Fetal Kidney	kidney
24	chr6:109799000-109803000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
25	chr6:109799200-109801200	Weak transcription	Aorta	Aorta
26	chr6:109799200-109801200	Weak transcription	Pancreas	Pancrea
27	chr6:109799200-109801400	Active TSS	GM12878-XiMat	blood
28	chr6:109799200-109801600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:109799200-109801600	Enhancers	Fetal Brain Male	brain
30	chr6:109799200-109801600	Weak transcription	Right Ventricle	heart
31	chr6:109799200-109802200	Enhancers	Brain Hippocampus Middle	brain
32	chr6:109799200-109802200	Weak transcription	Fetal Stomach	stomach
33	chr6:109799200-109803000	Weak transcription	Colonic Mucosa	Colon
34	chr6:109799200-109803400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:109799200-109803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:109799200-109803400	Weak transcription	Esophagus	oesophagus
37	chr6:109799400-109800800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:109799400-109800800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr6:109799400-109801200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:109799400-109801200	Weak transcription	Left Ventricle	heart
41	chr6:109799400-109801200	Weak transcription	Lung	lung
42	chr6:109799400-109801200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:109799600-109800600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:109799600-109800800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
45	chr6:109799600-109800800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:109799600-109801200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:109799600-109801200	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:109799600-109801200	Weak transcription	Psoas Muscle	Psoas
49	chr6:109799600-109801400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr6:109799600-109801400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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