Variant report

Variant	rs12658788
Chromosome Location	chr5:147041720-147041721
allele	A/G
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	POLR2A	chr5:147041623-147041892	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
JAKMIP2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10452517	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10452518	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10452530	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1159523	0.85[LWK][hapmap]
rs12657682	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12658834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13158025	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13162410	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1347137	0.81[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1347138	0.81[AFR][1000 genomes]
rs1347139	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1347140	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17106977	0.84[ASN][1000 genomes]
rs17107043	0.83[YRI][hapmap]
rs2053051	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116765	0.80[YRI][hapmap]
rs34147729	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35246628	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35416673	0.89[AFR][1000 genomes]
rs35542336	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147461	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147462	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147463	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147464	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4489050	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705188	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6859329	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6860455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883287	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887481	0.83[YRI][hapmap]
rs6896560	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73268170	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73268172	0.81[AFR][1000 genomes]
rs7709287	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7735403	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9325048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12658788	PRELID2	cis	parietal	SCAN
rs12658788	GRPEL2	cis	parietal	SCAN
rs12658788	CD74	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147009800-147051200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:147015400-147050000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:147016400-147052400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:147016600-147047400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:147021400-147042800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:147025200-147053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:147035800-147052800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:147036400-147042000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:147037200-147046600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:147038200-147044400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:147038200-147047800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:147038200-147048600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:147038600-147042000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:147038600-147042200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:147038800-147052200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:147038800-147053200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:147039000-147041800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:147039000-147042600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:147039200-147042200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:147039200-147047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:147039200-147051200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:147039200-147052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:147039600-147042400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:147039600-147050600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:147039600-147061800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:147039800-147046600	Weak transcription	Fetal Intestine Large	intestine
27	chr5:147040200-147042200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr5:147040200-147042400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:147040400-147042000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr5:147040600-147050400	Weak transcription	Fetal Thymus	thymus
31	chr5:147040800-147048200	Weak transcription	Fetal Brain Male	brain
32	chr5:147041000-147042200	Enhancers	Brain Angular Gyrus	brain
33	chr5:147041000-147046000	Weak transcription	Liver	Liver
34	chr5:147041000-147046800	Weak transcription	Primary T cells from cord blood	blood
35	chr5:147041000-147047400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:147041000-147047800	Weak transcription	Brain Substantia Nigra	brain
37	chr5:147041000-147048200	Weak transcription	Fetal Lung	lung
38	chr5:147041000-147049000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:147041000-147052800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:147041000-147053000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:147041200-147042000	Enhancers	Brain Hippocampus Middle	brain
42	chr5:147041200-147046000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:147041200-147046600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:147041200-147047800	Weak transcription	Brain Germinal Matrix	brain
45	chr5:147041200-147048800	Weak transcription	Thymus	Thymus
46	chr5:147041200-147050600	Weak transcription	Fetal Stomach	stomach
47	chr5:147041400-147042200	Enhancers	Brain Cingulate Gyrus	brain
48	chr5:147041400-147046600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:147041400-147047000	Weak transcription	Fetal Brain Female	brain
50	chr5:147041400-147047800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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