Variant report

Variant	rs12943480
Chromosome Location	chr17:15412038-15412039
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	chr17:15405961..15408797-chr17:15411656..15413886,2	K562	blood:
2	chr17:15411701..15413782-chr17:15416873..15418569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10153259	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12450262	0.85[ASN][1000 genomes]
rs12450302	0.85[ASN][1000 genomes]
rs12450921	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452965	0.81[ASN][1000 genomes]
rs12453117	0.81[ASN][1000 genomes]
rs12938444	0.85[ASN][1000 genomes]
rs12939314	0.89[JPT][hapmap]
rs12948266	1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs12953212	0.85[ASN][1000 genomes]
rs16940991	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17702522	1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs17702771	1.00[JPT][hapmap]
rs2013835	0.85[ASN][1000 genomes]
rs2532479	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2654261	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34236889	0.85[ASN][1000 genomes]
rs34358805	0.81[ASN][1000 genomes]
rs34453320	0.85[ASN][1000 genomes]
rs34818581	0.81[ASN][1000 genomes]
rs35078459	0.85[ASN][1000 genomes]
rs35406616	0.85[ASN][1000 genomes]
rs35448233	0.85[ASN][1000 genomes]
rs35699886	0.85[ASN][1000 genomes]
rs36097878	0.81[ASN][1000 genomes]
rs3852809	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3911955	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4054418	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4791625	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792619	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502459	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502461	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6502462	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71367505	0.83[ASN][1000 genomes]
rs716388	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7226342	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7359507	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8064461	0.94[ASN][1000 genomes]
rs8068610	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074456	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917567	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12943480	PMP22	cis	multi-tissue	Pritchard
rs12943480	CDRT4	cis	parietal	SCAN
rs12943480	AC005517.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12943480	FAM18B2	cis	parietal	SCAN
rs12943480	TRIM16	cis	parietal	SCAN
rs12943480	CDRT4	cis	cerebellum	SCAN
rs12943480	TEKT3	cis	cerebellum	SCAN
rs12943480	TEKT3	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
2	chr17:15383400-15455000	Weak transcription	Gastric	stomach
3	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
4	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
5	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
9	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
10	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:15400800-15413000	Weak transcription	NH-A	brain
12	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
13	chr17:15405400-15418200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr17:15405400-15419000	Weak transcription	Liver	Liver
15	chr17:15406000-15416800	Weak transcription	K562	blood
16	chr17:15406200-15414600	Weak transcription	Brain Angular Gyrus	brain
17	chr17:15406200-15414800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:15406200-15416800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:15406200-15420600	Weak transcription	Colonic Mucosa	Colon
20	chr17:15406600-15412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:15406600-15412800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr17:15406600-15413200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr17:15406600-15413400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:15406600-15413400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr17:15406600-15413400	Weak transcription	Brain Substantia Nigra	brain
26	chr17:15406600-15413400	Weak transcription	Osteobl	bone
27	chr17:15406600-15414400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr17:15406600-15414600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr17:15406600-15415000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:15406600-15416800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:15406600-15417000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:15406600-15417000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:15406600-15417000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr17:15406600-15417200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:15406600-15419000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:15406600-15419800	Weak transcription	NHEK	skin
37	chr17:15406600-15422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr17:15406800-15412600	Weak transcription	HUVEC	blood vessel
40	chr17:15406800-15412800	Weak transcription	Brain Anterior Caudate	brain
41	chr17:15406800-15413200	Weak transcription	Adipose Nuclei	Adipose
42	chr17:15406800-15413200	Weak transcription	A549	lung
43	chr17:15406800-15414400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr17:15406800-15414600	Weak transcription	Brain Hippocampus Middle	brain
45	chr17:15406800-15415400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:15406800-15415600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr17:15406800-15416400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:15406800-15417000	Weak transcription	Esophagus	oesophagus
49	chr17:15406800-15418200	Weak transcription	Placenta	Placenta
50	chr17:15406800-15418600	Weak transcription	Spleen	Spleen

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