Variant report

Variant	rs2704572
Chromosome Location	chr4:89812294-89812295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10019862	0.84[ASN][1000 genomes]
rs10028121	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10033435	0.81[ASN][1000 genomes]
rs10033476	0.81[ASN][1000 genomes]
rs1246630	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246633	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246637	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246638	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1246639	0.81[EUR][1000 genomes]
rs1246641	0.88[ASN][1000 genomes]
rs1272570	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13106968	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13148439	0.84[ASN][1000 genomes]
rs1379934	1.00[CHB][hapmap]
rs1458552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1458553	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1458555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1903004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1903009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2045516	0.88[ASN][1000 genomes]
rs2125410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2446295	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2446302	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2446309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464521	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2464527	0.81[AMR][1000 genomes]
rs2609254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2609274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2609278	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2609281	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2609284	0.81[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap]
rs2704588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704591	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704602	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704603	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28624770	0.84[ASN][1000 genomes]
rs28658282	0.84[ASN][1000 genomes]
rs2869965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869968	0.88[ASN][1000 genomes]
rs4498109	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59698155	0.84[ASN][1000 genomes]
rs7673427	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7697878	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922027	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs973680	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs987314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs993358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2704572	ABCG2	cis	cerebellum	SCAN
rs2704572	GRID2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89802200-89820600	Weak transcription	Aorta	Aorta
2	chr4:89802600-89812800	Weak transcription	K562	blood
3	chr4:89802600-89825600	Weak transcription	Ovary	ovary
4	chr4:89805400-89817600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:89809200-89828800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:89809400-89813400	Enhancers	Fetal Intestine Small	intestine
7	chr4:89811000-89813200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:89811400-89814400	Weak transcription	Placenta	Placenta
9	chr4:89811400-89814400	Weak transcription	Psoas Muscle	Psoas
10	chr4:89811600-89813000	Weak transcription	Fetal Intestine Large	intestine

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