Variant report

Variant	rs12512359
Chromosome Location	chr4:54023125-54023126
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54023036..54024737-chr4:54027112..54028617,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11133246	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133247	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11929903	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11939189	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11947928	0.81[AMR][1000 genomes]
rs12108246	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12499016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503963	0.98[ASN][1000 genomes]
rs12505661	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12507228	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12640471	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646150	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647441	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12650397	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082453	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17082476	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17082504	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17082529	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1987028	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001881	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34019927	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4299650	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4419530	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4421047	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4515221	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4529117	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72624192	0.84[AMR][1000 genomes]
rs72624193	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72624194	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73143456	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143458	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143484	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7688646	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7696426	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9761301	0.89[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
rs12512359	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53993800-54027800	Weak transcription	Fetal Stomach	stomach
2	chr4:53999000-54027800	Weak transcription	NHDF-Ad	bronchial
3	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:54005600-54023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:54007200-54030600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:54009600-54024000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:54010200-54034600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:54011400-54027800	Weak transcription	Aorta	Aorta
9	chr4:54011600-54027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:54011600-54027800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:54011600-54029200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:54011600-54030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:54011600-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:54011800-54023400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:54011800-54025800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:54011800-54026600	Weak transcription	Left Ventricle	heart
17	chr4:54011800-54031600	Weak transcription	Pancreas	Pancrea
18	chr4:54018000-54023400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:54018000-54028000	Weak transcription	Psoas Muscle	Psoas
20	chr4:54018000-54028200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:54018000-54035800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:54018200-54027400	Weak transcription	Liver	Liver
23	chr4:54019400-54042600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:54021800-54025600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:54022000-54023200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:54022000-54025600	Weak transcription	Primary B cells from cord blood	blood
27	chr4:54022000-54027800	Weak transcription	Fetal Kidney	kidney

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