Variant report

Variant	rs12192847
Chromosome Location	chr6:109801631-109801632
allele	A/G
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	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
3	chr6:109417075..109418905-chr6:109799494..109801799,2	K562	blood:
4	chr6:109774750..109777186-chr6:109800628..109803875,3	K562	blood:
5	chr6:109785634..109787468-chr6:109799694..109802286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135587	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

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	0.85[ASN][1000 genomes]
rs10457194	0.83[ASN][1000 genomes]
rs10457195	0.81[ASN][1000 genomes]
rs1048203	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782161	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782162	0.94[AFR][1000 genomes];0.94[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	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153174	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153175	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153176	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153177	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153180	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153181	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153183	0.85[ASN][1000 genomes]
rs11153188	0.81[ASN][1000 genomes]
rs11754455	0.85[ASN][1000 genomes]
rs11967108	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190920	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190996	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193493	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194061	0.81[ASN][1000 genomes]
rs12197114	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197180	0.84[ASN][1000 genomes]
rs12198938	0.85[ASN][1000 genomes]
rs12199154	0.85[ASN][1000 genomes]
rs12206928	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208933	0.81[EUR][1000 genomes]
rs12209691	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212476	0.85[ASN][1000 genomes]
rs12213313	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524273	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12524639	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12528822	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13201951	0.83[ASN][1000 genomes]
rs13203587	0.85[ASN][1000 genomes]
rs13212766	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13220915	0.85[ASN][1000 genomes]
rs1322816	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1358997	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1358998	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1406899	0.85[ASN][1000 genomes]
rs1476388	0.85[ASN][1000 genomes]
rs1546980	0.90[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	0.87[EUR][1000 genomes]
rs1923725	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998811	0.85[ASN][1000 genomes]
rs2024849	0.85[ASN][1000 genomes]
rs2024850	0.85[ASN][1000 genomes]
rs2024852	0.85[ASN][1000 genomes]
rs2024853	0.85[ASN][1000 genomes]
rs2208209	0.81[EUR][1000 genomes]
rs2236582	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275650	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277114	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	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757234	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778475	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778477	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799839	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3807005	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818934	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59056467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59906308	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68042406	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906216	0.83[ASN][1000 genomes]
rs6911838	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916579	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6926096	0.83[ASN][1000 genomes]
rs6929023	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7372	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749517	0.85[ASN][1000 genomes]
rs752262	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755941	0.85[ASN][1000 genomes]
rs7773095	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7773950	0.85[ASN][1000 genomes]
rs9320287	0.87[EUR][1000 genomes]
rs9480933	0.82[EUR][1000 genomes]
rs9480948	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480951	0.87[EUR][1000 genomes]
rs9480953	0.87[EUR][1000 genomes]
rs9480955	0.87[EUR][1000 genomes]
rs9480957	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487068	0.85[EUR][1000 genomes]
rs9487094	0.87[EUR][1000 genomes]
rs9487095	0.87[EUR][1000 genomes]
rs9487097	0.83[EUR][1000 genomes]
rs9487098	0.83[EUR][1000 genomes]
rs9487100	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9885646	0.87[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12192847	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12192847	SMPD2	cis	Whole Blood	GTEx
rs12192847	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12192847	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12192847	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	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	chr6:109789400-109803200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:109795200-109802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:109797800-109803400	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr6:109798000-109803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:109798000-109803400	Genic enhancers	Fetal Thymus	thymus
8	chr6:109798200-109802200	Weak transcription	Gastric	stomach
9	chr6:109798200-109803000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:109798600-109802600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr6:109798600-109802800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
12	chr6:109798600-109803400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr6:109798800-109802400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr6:109799000-109801800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:109799000-109801800	Weak transcription	Fetal Kidney	kidney
16	chr6:109799000-109803000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
17	chr6:109799200-109802200	Enhancers	Brain Hippocampus Middle	brain
18	chr6:109799200-109802200	Weak transcription	Fetal Stomach	stomach
19	chr6:109799200-109803000	Weak transcription	Colonic Mucosa	Colon
20	chr6:109799200-109803400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:109799200-109803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:109799200-109803400	Weak transcription	Esophagus	oesophagus
23	chr6:109799600-109802200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr6:109799600-109803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:109799800-109801800	Enhancers	Colon Smooth Muscle	Colon
26	chr6:109799800-109803200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
27	chr6:109799800-109803400	Enhancers	Ovary	ovary
28	chr6:109800000-109803200	Genic enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:109800000-109803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:109800200-109802000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:109800200-109803000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:109800400-109801800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr6:109800400-109802000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
34	chr6:109800400-109803200	Transcr. at gene 5' and 3'	K562	blood
35	chr6:109800600-109801800	Active TSS	A549	lung
36	chr6:109800600-109802600	Genic enhancers	Fetal Brain Female	brain
37	chr6:109800600-109803200	Genic enhancers	Primary hematopoietic stem cells	blood
38	chr6:109800800-109801800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:109800800-109801800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:109800800-109801800	Enhancers	Brain Angular Gyrus	brain
41	chr6:109800800-109801800	Enhancers	Brain Substantia Nigra	brain
42	chr6:109800800-109801800	Weak transcription	Stomach Mucosa	stomach
43	chr6:109800800-109801800	Strong transcription	HMEC	breast
44	chr6:109800800-109801800	Strong transcription	NH-A	brain
45	chr6:109800800-109802000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:109800800-109802200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:109800800-109802800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:109800800-109803000	Genic enhancers	NHDF-Ad	bronchial
49	chr6:109800800-109803200	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr6:109800800-109803400	Enhancers	Thymus	Thymus

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