Variant report

Variant	rs13119090
Chromosome Location	chr4:143578523-143578524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143577881..143580712-chr4:143582795..143584320,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1017527	0.93[CHD][hapmap]
rs1031104	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10857397	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11100752	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1116690	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723809	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942731	0.84[YRI][hapmap]
rs11943397	0.88[CHD][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11944455	0.89[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233703	0.86[ASN][1000 genomes]
rs12500698	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508480	0.88[ASN][1000 genomes]
rs13102191	0.87[ASN][1000 genomes]
rs13109603	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109664	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114452	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13125853	0.90[ASN][1000 genomes]
rs13133181	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13147451	0.81[JPT][hapmap]
rs13149611	0.94[CHD][hapmap]
rs1364921	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1364922	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1364925	0.82[CHB][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs1373041	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1443187	0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1443188	0.85[ASN][1000 genomes]
rs1443190	0.94[CHD][hapmap]
rs1443191	0.82[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17016768	0.85[JPT][hapmap]
rs1899565	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1961836	0.86[ASN][1000 genomes]
rs2017146	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2083781	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2120158	0.83[CHD][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2165820	0.82[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2197216	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2217017	0.87[ASN][1000 genomes]
rs2874870	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2874871	0.81[CHB][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs331945	0.85[JPT][hapmap]
rs6537123	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6830053	0.80[CEU][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6830886	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6831966	0.84[ASN][1000 genomes]
rs6839894	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7437824	0.88[ASN][1000 genomes]
rs7441478	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666140	0.85[JPT][hapmap]
rs7675305	0.94[CHD][hapmap]
rs7680076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680631	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7682731	0.94[CHD][hapmap]
rs7685086	0.85[ASN][1000 genomes]
rs7688435	0.94[CHD][hapmap]
rs7695514	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698691	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978361	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs979194	0.95[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs979195	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs979196	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13119090	C4orf49	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143574400-143583800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:143575400-143579000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
3	chr4:143575400-143583800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:143575600-143582400	ZNF genes & repeats	Dnd41	blood
5	chr4:143575800-143579800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143576000-143578800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr4:143576200-143579800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:143577200-143578600	ZNF genes & repeats	Fetal Heart	heart
9	chr4:143577200-143580000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr4:143577800-143578600	ZNF genes & repeats	Left Ventricle	heart
11	chr4:143578200-143578600	ZNF genes & repeats	Brain Anterior Caudate	brain

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