Variant report

Variant	rs12594742
Chromosome Location	chr15:58958465-58958466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58953177..58955880-chr15:58958454..58961862,3	K562	blood:
2	chr15:58958405..58960158-chr15:58960218..58962844,2	MCF-7	breast:
3	chr15:58957306..58961861-chr15:58967060..58970416,4	K562	blood:
4	chr15:58956671..58958559-chr15:58959977..58961761,2	K562	blood:
5	chr15:58950082..58952311-chr15:58956735..58959470,2	K562	blood:
6	chr15:58949134..58952311-chr15:58956735..58961509,4	K562	blood:
7	chr15:58932722..58935543-chr15:58957168..58958694,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11071391	0.94[CEU][hapmap]
rs11071392	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11071393	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12437457	0.94[CEU][hapmap]
rs12437998	0.82[AMR][1000 genomes]
rs12438487	1.00[CEU][hapmap]
rs12438810	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12439231	0.88[CEU][hapmap]
rs12439632	0.81[CEU][hapmap]
rs12441313	0.88[CEU][hapmap]
rs12441912	0.86[CEU][hapmap]
rs12442451	0.88[CEU][hapmap]
rs12591543	0.82[EUR][1000 genomes]
rs12592332	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12592750	0.81[AMR][1000 genomes]
rs12708455	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs12901989	0.94[CEU][hapmap]
rs12905110	0.94[CEU][hapmap]
rs12906705	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12906714	0.88[CEU][hapmap]
rs12907237	0.86[CEU][hapmap]
rs12908165	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908261	0.88[CEU][hapmap]
rs12908449	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12912286	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs12913383	0.83[CEU][hapmap];0.87[MKK][hapmap]
rs12915950	0.80[EUR][1000 genomes]
rs12917577	0.94[CEU][hapmap]
rs16940587	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs16940589	0.94[CEU][hapmap]
rs16940629	0.81[YRI][hapmap]
rs16940647	1.00[CEU][hapmap]
rs16940651	1.00[CEU][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17236194	0.88[CEU][hapmap]
rs17301864	0.82[CEU][hapmap]
rs2052804	0.81[AMR][1000 genomes]
rs2052805	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs2305421	0.94[CEU][hapmap];0.81[GIH][hapmap];0.80[AMR][1000 genomes]
rs28455654	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28573205	0.81[AMR][1000 genomes]
rs28600144	0.80[EUR][1000 genomes]
rs28637832	0.80[EUR][1000 genomes]
rs28639679	0.81[EUR][1000 genomes]
rs28678478	0.81[AMR][1000 genomes]
rs28724298	0.83[EUR][1000 genomes]
rs28734088	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35499736	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6074	0.82[CEU][hapmap]
rs6494030	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6494031	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6494032	0.83[EUR][1000 genomes]
rs6494033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494034	0.88[CEU][hapmap]
rs6494038	0.94[CEU][hapmap]
rs7163733	0.94[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs7165035	1.00[CEU][hapmap]
rs7165402	1.00[CEU][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7166076	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs7166325	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7167528	0.94[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7170314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174175	0.81[AMR][1000 genomes]
rs7174386	1.00[CEU][hapmap]
rs7174414	0.93[CEU][hapmap]
rs7178954	0.81[AMR][1000 genomes]
rs7180550	0.80[EUR][1000 genomes]
rs8026668	0.83[EUR][1000 genomes]
rs8029805	0.88[CEU][hapmap]
rs8033691	0.88[CEU][hapmap]
rs8035960	0.83[EUR][1000 genomes]
rs8036005	0.94[CEU][hapmap]
rs8039791	0.83[CEU][hapmap]
rs8040358	0.81[EUR][1000 genomes]
rs9302203	1.00[CEU][hapmap]
rs9635351	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs9744518	0.82[EUR][1000 genomes]
rs9920310	0.81[EUR][1000 genomes]
rs9920720	1.00[CEU][hapmap]
rs9921024	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12594742	PIGB	cis	cerebellum	SCAN
rs12594742	RNF111	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
8	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
9	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:58921600-58959200	Weak transcription	NHLF	lung
11	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
12	chr15:58921800-58970400	Weak transcription	Stomach Mucosa	stomach
13	chr15:58922200-58959000	Weak transcription	HUVEC	blood vessel
14	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
15	chr15:58923400-58982800	Weak transcription	Lung	lung
16	chr15:58924000-58960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:58933600-58959000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:58934200-58976400	Weak transcription	Psoas Muscle	Psoas
20	chr15:58936000-58977000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:58936200-58991400	Weak transcription	HMEC	breast
22	chr15:58945600-58959400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:58946400-58958600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:58947000-58959000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:58947200-58959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:58947800-58971800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:58947800-58976400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:58948000-58959400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:58948400-58959200	Weak transcription	NH-A	brain
30	chr15:58949400-58976400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:58951000-58959600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:58951200-58987000	Weak transcription	NHEK	skin
33	chr15:58951400-58959400	Strong transcription	Fetal Thymus	thymus
34	chr15:58951600-58961400	Weak transcription	Fetal Lung	lung
35	chr15:58951600-58976400	Weak transcription	GM12878-XiMat	blood
36	chr15:58951600-58981800	Weak transcription	Fetal Brain Male	brain
37	chr15:58951800-58960200	Weak transcription	Fetal Heart	heart
38	chr15:58952200-58958800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr15:58952600-58959200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:58952600-58959400	Weak transcription	HSMMtube	muscle
41	chr15:58952600-58960600	Weak transcription	Fetal Intestine Small	intestine
42	chr15:58953000-58958600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:58955000-58971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:58955200-58958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:58955200-58959200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:58955200-58971800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:58955200-58971800	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:58955200-58971800	Weak transcription	Fetal Stomach	stomach
49	chr15:58955200-58971800	Weak transcription	Left Ventricle	heart
50	chr15:58955200-58976400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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