Variant report

Variant	rs4261974
Chromosome Location	chr4:119870169-119870170
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10017229	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518317	0.91[EUR][1000 genomes]
rs13151719	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17050228	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17050240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261234	0.91[EUR][1000 genomes]
rs17327171	0.86[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2389694	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34123613	0.89[ASN][1000 genomes]
rs4299565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834729	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs67109496	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72671630	0.88[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	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
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4261974	USP53	cis	cerebellum	SCAN
rs4261974	PRSS12	cis	parietal	SCAN
rs4261974	EXOSC9	cis	parietal	SCAN
rs4261974	USP53	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119858800-119871600	Weak transcription	Psoas Muscle	Psoas
2	chr4:119863400-119871600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:119863600-119871400	Weak transcription	Right Ventricle	heart
4	chr4:119864000-119871400	Weak transcription	Left Ventricle	heart
5	chr4:119867200-119871400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:119868400-119870400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:119868600-119871400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:119868600-119871400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:119868600-119872200	Weak transcription	Fetal Heart	heart
10	chr4:119868800-119870600	Enhancers	Colon Smooth Muscle	Colon
11	chr4:119868800-119871400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:119868800-119871400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:119868800-119886000	Weak transcription	Fetal Stomach	stomach
14	chr4:119869000-119870600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:119869400-119870400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:119869600-119870400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr4:119869600-119870400	Enhancers	Ovary	ovary
18	chr4:119869800-119870200	Enhancers	Small Intestine	intestine
19	chr4:119869800-119870400	Enhancers	H9 Cell Line	embryonic stem cell
20	chr4:119869800-119870400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:119869800-119870600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr4:119869800-119871400	Weak transcription	Lung	lung
23	chr4:119870000-119870200	Enhancers	Aorta	Aorta
24	chr4:119870000-119870400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr4:119870000-119870400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:119870000-119871600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:119870000-119874400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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