Variant report

Variant	rs12902119
Chromosome Location	chr15:58756554-58756555
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58754820..58757599-chr15:58758355..58762013,3	K562	blood:
2	chr15:58750305..58752654-chr15:58755983..58757859,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10518978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634902	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12591216	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12592407	0.90[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12593736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593880	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12594222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12595191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903955	0.81[ASN][1000 genomes]
rs12904507	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12906459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908427	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12910028	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12910602	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17190580	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17190587	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2414581	0.85[ASN][1000 genomes]
rs28478642	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28713618	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899630	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34053638	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34225834	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34297592	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34570549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577128	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34744603	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35633916	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35732576	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35771822	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35795657	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775053	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6494009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494010	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71478667	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71478668	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71478670	0.81[ASN][1000 genomes]
rs71478671	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71478672	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7162384	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7162603	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7165752	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169744	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172681	1.00[YRI][hapmap]
rs7174539	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029592	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8029837	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8041525	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1043362	chr15:58726337-58756571	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12902119	KIAA1370	cis	parietal	SCAN
rs12902119	KIAA1370	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58737400-58761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
3	chr15:58751200-58757200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:58751600-58757800	Weak transcription	Fetal Kidney	kidney
5	chr15:58752000-58757800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:58752000-58757800	Weak transcription	NHLF	lung
7	chr15:58752400-58761800	Weak transcription	Right Atrium	heart
8	chr15:58752600-58760200	Weak transcription	Hela-S3	cervix
9	chr15:58752800-58757800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:58752800-58757800	Weak transcription	HSMM	muscle
11	chr15:58752800-58765000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:58753000-58760400	Weak transcription	Pancreas	Pancrea
13	chr15:58753800-58757000	Enhancers	Thymus	Thymus
14	chr15:58754000-58759400	Enhancers	HepG2	liver
15	chr15:58754000-58760000	Weak transcription	Spleen	Spleen
16	chr15:58754200-58756600	Enhancers	Primary T cells from cord blood	blood
17	chr15:58754400-58756600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:58754600-58756600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr15:58754600-58759400	Enhancers	Liver	Liver
20	chr15:58754800-58757000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:58754800-58757000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:58755000-58759600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:58755200-58756600	Enhancers	HSMMtube	muscle
24	chr15:58755200-58758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:58755200-58758000	Enhancers	Dnd41	blood
26	chr15:58755200-58759400	Weak transcription	Placenta	Placenta
27	chr15:58755400-58759400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:58755400-58759400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:58755400-58760400	Weak transcription	Fetal Intestine Small	intestine
30	chr15:58755400-58765000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:58755400-58765000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:58755600-58757800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:58755600-58759400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:58755600-58759400	Weak transcription	Fetal Intestine Large	intestine
35	chr15:58755600-58759400	Weak transcription	Stomach Mucosa	stomach
36	chr15:58755600-58759400	Weak transcription	K562	blood
37	chr15:58755600-58759800	Enhancers	GM12878-XiMat	blood
38	chr15:58755600-58759800	Weak transcription	NH-A	brain
39	chr15:58755600-58760400	Weak transcription	NHEK	skin
40	chr15:58755600-58760800	Weak transcription	HMEC	breast
41	chr15:58755600-58761400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:58755600-58763600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:58755800-58761000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:58755800-58761400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:58755800-58762200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:58755800-58765800	Weak transcription	Gastric	stomach
47	chr15:58756000-58756600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr15:58756000-58759400	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:58756000-58759400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:58756200-58756800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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