Variant report

Variant	rs12503963
Chromosome Location	chr4:54052613-54052614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11133246	0.97[ASN][1000 genomes]
rs11133247	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929903	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11939189	1.00[CEU][hapmap];0.87[ASN][1000 genomes]
rs11947928	0.88[AFR][1000 genomes]
rs12108246	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12499016	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505661	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12507228	0.88[ASN][1000 genomes]
rs12512359	0.98[ASN][1000 genomes]
rs12640471	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12646150	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12647441	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12650397	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082476	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17082504	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082529	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs1987028	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34019927	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299650	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4419530	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4421047	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4515221	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4529117	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73143456	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143458	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143484	1.00[ASN][1000 genomes]
rs7688646	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9761301	0.82[EUR][1000 genomes];0.91[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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12503963	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54038800-54054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
4	chr4:54049800-54053600	Weak transcription	NHLF	lung
5	chr4:54050000-54053000	Strong transcription	Primary B cells from cord blood	blood
6	chr4:54050200-54061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:54050400-54062400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:54050800-54053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:54052000-54053000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:54052000-54053400	Enhancers	Fetal Lung	lung
12	chr4:54052000-54054200	Enhancers	Liver	Liver
13	chr4:54052000-54054400	Enhancers	Fetal Kidney	kidney
14	chr4:54052000-54054400	Enhancers	Osteobl	bone
15	chr4:54052000-54055400	Enhancers	Fetal Intestine Large	intestine
16	chr4:54052000-54055800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:54052000-54056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:54052200-54052800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:54052200-54052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:54052200-54052800	Enhancers	Fetal Stomach	stomach
21	chr4:54052200-54052800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:54052200-54053000	Enhancers	HSMM	muscle
23	chr4:54052200-54053200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:54052200-54054400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:54052200-54054400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:54052200-54054400	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr4:54052200-54054600	Enhancers	K562	blood
28	chr4:54052200-54055800	Enhancers	HepG2	liver
29	chr4:54052200-54056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:54052200-54056600	Enhancers	NHDF-Ad	bronchial
31	chr4:54052400-54052800	Enhancers	Brain Anterior Caudate	brain
32	chr4:54052400-54052800	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:54052400-54052800	Weak transcription	HSMMtube	muscle
34	chr4:54052400-54053200	Enhancers	Brain Substantia Nigra	brain
35	chr4:54052400-54053600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:54052400-54054400	Weak transcription	Ovary	ovary
37	chr4:54052400-54056000	Enhancers	NH-A	brain
38	chr4:54052400-54065800	Weak transcription	Aorta	Aorta
39	chr4:54052600-54052800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:54052600-54053000	Enhancers	Brain Angular Gyrus	brain
41	chr4:54052600-54053000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr4:54052600-54054200	Weak transcription	Fetal Intestine Small	intestine

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