Variant report

Variant	rs12591418
Chromosome Location	chr15:78340539-78340540
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78326751..78329240-chr15:78339256..78341988,2	K562	blood:
2	chr15:78337006..78339550-chr15:78339684..78342171,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1004855	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10519181	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs11072716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638311	0.83[ASN][1000 genomes]
rs11852768	0.99[ASN][1000 genomes]
rs12148365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12594823	1.00[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes]
rs12899061	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs12907701	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs12916362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1348257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs17477813	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs1837913	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap]
rs2028546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2044099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs2867985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2903702	0.98[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs4886553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886555	0.96[ASN][1000 genomes]
rs4886994	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4886996	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56317829	0.93[ASN][1000 genomes]
rs57220134	0.97[ASN][1000 genomes]
rs58578288	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62011511	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166819	0.99[ASN][1000 genomes]
rs7170746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs7181594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029562	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs8030999	0.94[ASW][hapmap];0.84[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs9047	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12591418	CLK3	cis	cerebellum	SCAN
rs12591418	ISL2	cis	parietal	SCAN
rs12591418	HEXA	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78321200-78343800	Weak transcription	NHEK	skin
11	chr15:78322200-78341000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:78327800-78342000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr15:78328000-78341800	Weak transcription	Fetal Brain Male	brain
15	chr15:78328400-78342200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:78328600-78342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:78329000-78342400	Weak transcription	Fetal Heart	heart
18	chr15:78330600-78342800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
20	chr15:78331400-78348600	Weak transcription	A549	lung
21	chr15:78331600-78348600	Weak transcription	K562	blood
22	chr15:78332000-78342200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:78332600-78342000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:78332800-78343000	Weak transcription	Hela-S3	cervix
25	chr15:78334800-78342200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:78335000-78342000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:78336600-78344400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:78336800-78342400	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:78337000-78347800	Weak transcription	Ovary	ovary
30	chr15:78337200-78341800	Weak transcription	Fetal Brain Female	brain
31	chr15:78337200-78342800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:78337200-78344400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:78337400-78342000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr15:78337800-78344600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:78338200-78344400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:78338600-78345400	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:78338800-78340800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr15:78338800-78341000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:78338800-78341200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:78338800-78341200	Enhancers	Colonic Mucosa	Colon
41	chr15:78338800-78341400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr15:78338800-78341800	Genic enhancers	Placenta	Placenta
43	chr15:78338800-78342200	Enhancers	Adipose Nuclei	Adipose
44	chr15:78338800-78342600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:78338800-78344600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr15:78338800-78344800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:78338800-78347000	Genic enhancers	Fetal Thymus	thymus
48	chr15:78339000-78340600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:78339000-78340600	Enhancers	Fetal Intestine Large	intestine
50	chr15:78339000-78341000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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