Variant report

Variant	rs3885192
Chromosome Location	chr4:119788343-119788344
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	chr4:119786405..119788908-chr4:119826378..119828517,2	MCF-7	breast:
2	chr4:119774467..119777220-chr4:119785721..119788417,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1019696	0.82[ASW][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11098453	0.82[JPT][hapmap]
rs11098459	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11098460	0.85[ASN][1000 genomes]
rs11722846	1.00[YRI][hapmap]
rs11931472	1.00[YRI][hapmap]
rs12512594	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12643205	0.82[JPT][hapmap]
rs13139244	0.82[JPT][hapmap]
rs1365549	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1365550	0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1365551	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2114461	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775839	0.82[ASW][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs4833592	0.90[JPT][hapmap]
rs4833593	0.82[JPT][hapmap]
rs4834706	0.82[JPT][hapmap]
rs4834710	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836897	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7375858	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3885192	SEC24D	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119780200-119788400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:119786400-119791200	Weak transcription	Right Atrium	heart
3	chr4:119786600-119791200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:119786800-119790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:119786800-119790800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:119786800-119790800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:119786800-119791000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:119786800-119791000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:119786800-119791000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:119786800-119791000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:119786800-119791000	Weak transcription	HSMM	muscle
12	chr4:119786800-119791200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:119786800-119791200	Weak transcription	Adipose Nuclei	Adipose
14	chr4:119786800-119793200	Weak transcription	NHEK	skin
15	chr4:119787000-119790600	Weak transcription	HUVEC	blood vessel
16	chr4:119787600-119788600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:119787600-119790600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:119787800-119790800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:119787800-119791000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:119788200-119788400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:119788200-119788600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:119788200-119789200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:119788200-119789200	Enhancers	NHDF-Ad	bronchial
24	chr4:119788200-119790600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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