Variant report

Variant	rs12497427
Chromosome Location	chr3:43125481-43125482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43123950..43126006-chr3:43128155..43130598,2	K562	blood:

Variant related genes	Relation type
ENSG00000227245	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1072822	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1125065	0.84[GIH][hapmap];0.86[MEX][hapmap]
rs12233614	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12485530	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485578	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523125	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523126	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1566422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17391761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470089	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815070	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];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1949583	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1949584	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs488069	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55764298	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55819365	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55945909	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55954171	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796161	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074962	0.80[EUR][1000 genomes]
rs7624799	1.00[LWK][hapmap]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12497427	CCDC13	cis	parietal	SCAN
rs12497427	ABHD5	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43118200-43128000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43118600-43127800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:43119000-43129600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:43119400-43126200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:43119400-43129800	Weak transcription	Fetal Kidney	kidney
6	chr3:43119600-43130400	Weak transcription	Hela-S3	cervix
7	chr3:43119600-43135000	Weak transcription	Psoas Muscle	Psoas
8	chr3:43119800-43143800	Weak transcription	Fetal Heart	heart
9	chr3:43120000-43125800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:43120400-43125600	Weak transcription	A549	lung
11	chr3:43122000-43126000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:43122400-43134400	Weak transcription	HepG2	liver
13	chr3:43122400-43145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:43122600-43128200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:43122600-43130200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:43122600-43145200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:43122800-43125600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:43122800-43127800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:43122800-43128600	Weak transcription	Liver	Liver
20	chr3:43122800-43129200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:43122800-43132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:43122800-43132200	Weak transcription	Fetal Lung	lung
23	chr3:43122800-43133000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:43122800-43134800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:43122800-43136000	Weak transcription	Pancreas	Pancrea
26	chr3:43122800-43136400	Weak transcription	HSMMtube	muscle
27	chr3:43122800-43145600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:43123000-43125600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:43123000-43128000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:43123000-43129600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:43123000-43132200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:43123000-43132600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:43123000-43135200	Weak transcription	Brain Angular Gyrus	brain
34	chr3:43123000-43136000	Weak transcription	Right Ventricle	heart
35	chr3:43123000-43144400	Weak transcription	Fetal Intestine Large	intestine
36	chr3:43123000-43146400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:43123000-43146600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:43123200-43125800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:43123200-43127800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:43123200-43132000	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:43123200-43140400	Weak transcription	Gastric	stomach
42	chr3:43123200-43144400	Weak transcription	Spleen	Spleen
43	chr3:43123200-43145000	Weak transcription	Adipose Nuclei	Adipose
44	chr3:43123400-43125600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:43123400-43130000	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:43123400-43146400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:43123600-43127000	Weak transcription	Brain Germinal Matrix	brain
48	chr3:43123600-43128800	Weak transcription	Esophagus	oesophagus
49	chr3:43123600-43135000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:43123600-43135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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