Variant report

Variant	rs12895070
Chromosome Location	chr14:56092719-56092720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56090621..56092571-chr14:56092593..56095117,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10136408	0.86[CEU][hapmap]
rs10146870	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10444721	0.81[JPT][hapmap]
rs10483644	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10483649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12432344	0.83[EUR][1000 genomes]
rs12432588	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12432887	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12433592	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12434624	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12434660	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12434799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12435643	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12587700	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12587705	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12587735	0.81[JPT][hapmap]
rs12588185	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12589864	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12589867	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12590388	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12590936	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12882850	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12885864	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12888809	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12891489	0.86[CEU][hapmap]
rs12891526	0.84[ASN][1000 genomes]
rs12897227	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17128610	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128655	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17128657	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17128677	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17128684	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17128690	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1951887	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1951889	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1951890	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2093800	0.94[ASN][1000 genomes]
rs2252189	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2274076	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274078	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2274079	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296182	0.85[JPT][hapmap]
rs2341889	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28458791	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28703642	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34023572	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34111199	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34118806	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34184813	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34408323	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34548095	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34697059	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34706911	0.80[ASN][1000 genomes]
rs34709110	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34931260	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35047443	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35094494	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35420484	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35451981	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35531912	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35535838	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35560341	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35790844	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3765515	0.81[JPT][hapmap]
rs4457912	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs55760841	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56229542	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60233569	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61381603	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573051	0.89[ASN][1000 genomes]
rs6573053	0.81[JPT][hapmap]
rs6573054	0.81[JPT][hapmap]
rs68127620	0.93[ASN][1000 genomes]
rs7154548	0.94[ASN][1000 genomes]
rs7156566	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72719463	0.87[ASN][1000 genomes]
rs8003149	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8006443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8007183	0.94[ASN][1000 genomes]
rs8007832	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs8008764	0.94[ASN][1000 genomes]
rs8011252	0.81[ASN][1000 genomes]
rs8015588	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12895070	NAA30	cis	cerebellum	SCAN
rs12895070	GCH1	cis	cerebellum	SCAN
rs12895070	GCH1	cis	parietal	SCAN
rs12895070	KTN1	cis	cerebellum	SCAN
rs12895070	KTN1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56078600-56148600	Weak transcription	Stomach Mucosa	stomach
2	chr14:56078800-56095400	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr14:56079200-56095200	Strong transcription	Primary T cells from cord blood	blood
4	chr14:56079800-56111400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr14:56080200-56097800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr14:56080800-56110800	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr14:56086000-56093400	Strong transcription	A549	lung
8	chr14:56086800-56094400	Weak transcription	NHDF-Ad	bronchial
9	chr14:56087400-56092800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:56087400-56093400	Weak transcription	K562	blood
11	chr14:56087400-56094400	Weak transcription	HepG2	liver
12	chr14:56087400-56094800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:56087400-56111800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:56087400-56112200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr14:56087400-56132200	Strong transcription	Dnd41	blood
16	chr14:56087600-56099000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr14:56087600-56099400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:56087600-56100400	Weak transcription	Right Ventricle	heart
19	chr14:56087600-56100600	Weak transcription	Fetal Intestine Small	intestine
20	chr14:56087600-56101400	Weak transcription	Pancreas	Pancrea
21	chr14:56087600-56107400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:56087600-56110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:56087800-56093800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:56088000-56093600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:56088000-56094400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr14:56088000-56095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr14:56088000-56096800	Weak transcription	Small Intestine	intestine
29	chr14:56088000-56096800	Weak transcription	NHLF	lung
30	chr14:56088000-56101200	Weak transcription	Esophagus	oesophagus
31	chr14:56088000-56101600	Weak transcription	Fetal Brain Male	brain
32	chr14:56088000-56103600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:56088200-56092800	Strong transcription	GM12878-XiMat	blood
34	chr14:56088200-56093400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr14:56088200-56094200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr14:56088200-56094400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr14:56088200-56094400	Weak transcription	Fetal Kidney	kidney
38	chr14:56088200-56096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr14:56088200-56098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:56088200-56104000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr14:56088200-56108600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr14:56088200-56129400	Weak transcription	Spleen	Spleen
43	chr14:56088200-56132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:56088400-56093000	Weak transcription	Brain Substantia Nigra	brain
45	chr14:56088400-56094200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr14:56088400-56094400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr14:56088400-56094400	Weak transcription	Fetal Lung	lung
48	chr14:56088400-56094400	Weak transcription	Thymus	Thymus
49	chr14:56088400-56094600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:56088400-56096800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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