Variant report

Variant	rs4952077
Chromosome Location	chr2:31502382-31502383
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	chr2:31500916..31502879-chr2:31504188..31506195,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1010477	0.91[ASN][1000 genomes]
rs10175943	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124256	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683836	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988379	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474941	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145036	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365559	0.86[AMR][1000 genomes]
rs4366947	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951976	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951977	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952078	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586245	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs590009	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs598204	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs602322	0.91[ASN][1000 genomes]
rs604127	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs604986	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs631396	0.91[ASN][1000 genomes]
rs637911	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644417	0.82[ASN][1000 genomes]
rs644736	0.82[ASN][1000 genomes]
rs646103	0.86[ASN][1000 genomes]
rs646200	0.86[ASN][1000 genomes]
rs6543622	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661015	0.91[ASN][1000 genomes]
rs674791	0.91[ASN][1000 genomes]
rs684967	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581173	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9678585	0.92[AMR][1000 genomes];0.85[EUR][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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4952077	NLRC4	cis	cerebellum	SCAN
rs4952077	IFT172	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31486600-31510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:31490000-31502400	Weak transcription	Spleen	Spleen
3	chr2:31492400-31507800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:31492800-31510600	Weak transcription	Aorta	Aorta
5	chr2:31494400-31505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:31495800-31509800	Weak transcription	Esophagus	oesophagus
7	chr2:31497000-31510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:31497200-31502600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:31501400-31505600	Weak transcription	HUVEC	blood vessel
10	chr2:31501600-31502400	Enhancers	Lung	lung
11	chr2:31502000-31502600	Enhancers	Placenta	Placenta
12	chr2:31502000-31505600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:31502200-31504200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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