Variant report

Variant	rs4713001
Chromosome Location	chr6:26487310-26487311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26477480..26482334-chr6:26483111..26488376,9	K562	blood:
2	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
3	chr6:26487097..26490351-chr6:26520890..26522869,3	K562	blood:
4	chr6:26282904..26284405-chr6:26486849..26489671,2	K562	blood:
5	chr6:26457050..26459472-chr6:26486293..26488902,2	K562	blood:
6	chr6:26487017..26489284-chr6:26492809..26495203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10447390	0.86[CEU][hapmap]
rs10447391	0.86[CEU][hapmap]
rs10456047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807008	1.00[CEU][hapmap]
rs10946820	0.86[CEU][hapmap]
rs10946821	0.86[CEU][hapmap]
rs10946823	0.92[CEU][hapmap]
rs10946824	0.86[CEU][hapmap]
rs10946825	0.91[CEU][hapmap]
rs10946826	0.86[CEU][hapmap]
rs10946827	0.85[CEU][hapmap]
rs10946829	0.86[CEU][hapmap]
rs10946832	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs10946842	1.00[JPT][hapmap]
rs1131936	0.93[CEU][hapmap]
rs11753257	1.00[YRI][hapmap]
rs11760103	1.00[YRI][hapmap]
rs12191917	0.86[CEU][hapmap]
rs12193283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194001	0.83[CEU][hapmap]
rs12194036	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12194073	0.86[CEU][hapmap]
rs12196371	1.00[CEU][hapmap]
rs12197304	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198993	0.86[CEU][hapmap]
rs12201546	0.86[CEU][hapmap]
rs12205310	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12206812	0.86[CEU][hapmap]
rs12207930	0.86[CEU][hapmap]
rs12208211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208272	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208788	0.93[CEU][hapmap]
rs12211872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214444	1.00[CEU][hapmap]
rs12214486	0.86[CEU][hapmap]
rs12214924	0.86[CEU][hapmap]
rs12661560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664899	0.93[CEU][hapmap]
rs17537465	0.93[CEU][hapmap]
rs17539219	0.86[CEU][hapmap]
rs17610161	1.00[CEU][hapmap]
rs17611220	0.86[CEU][hapmap]
rs17611438	0.85[CEU][hapmap]
rs1884945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393652	0.86[CEU][hapmap]
rs2393664	0.81[CEU][hapmap]
rs2893844	0.85[CEU][hapmap]
rs2893845	0.86[CEU][hapmap]
rs2893847	0.86[CEU][hapmap]
rs2893848	0.86[CEU][hapmap]
rs2893849	0.93[CEU][hapmap]
rs2893856	0.93[CEU][hapmap]
rs2893857	1.00[ASW][hapmap];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];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3198487	0.85[CEU][hapmap]
rs3208734	0.85[CEU][hapmap]
rs3757143	1.00[YRI][hapmap]
rs3846843	0.86[CEU][hapmap]
rs3846844	0.86[CEU][hapmap]
rs3846847	0.86[CEU][hapmap]
rs3846848	0.86[CEU][hapmap]
rs3846849	0.86[CEU][hapmap]
rs3902051	0.93[CEU][hapmap]
rs4083469	0.86[CEU][hapmap]
rs4609015	0.86[CEU][hapmap]
rs4711108	1.00[CEU][hapmap]
rs4711109	0.86[CEU][hapmap]
rs4711110	1.00[CEU][hapmap]
rs4711111	0.86[CEU][hapmap]
rs4712986	0.93[CEU][hapmap]
rs4712988	0.93[CEU][hapmap]
rs4712990	1.00[CEU][hapmap]
rs4712993	0.86[CEU][hapmap]
rs4712994	0.86[CEU][hapmap]
rs4712996	0.86[CEU][hapmap]
rs4712999	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4713000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713011	1.00[JPT][hapmap]
rs56034653	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6456722	0.85[CEU][hapmap]
rs6456724	0.93[CEU][hapmap]
rs6900725	0.86[CEU][hapmap]
rs6901245	0.84[CEU][hapmap]
rs6907302	0.86[AMR][1000 genomes]
rs6910023	0.86[CEU][hapmap]
rs6912934	0.93[CEU][hapmap]
rs6920986	0.86[CEU][hapmap]
rs6926878	0.86[CEU][hapmap]
rs6928454	0.86[CEU][hapmap]
rs6929846	0.86[CEU][hapmap]
rs72843766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355	0.93[CEU][hapmap]
rs7356849	0.93[CEU][hapmap]
rs7744254	0.86[CEU][hapmap]
rs7745238	0.86[CEU][hapmap]
rs7745767	0.86[CEU][hapmap]
rs7751280	0.86[CEU][hapmap]
rs7768108	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7770214	0.86[CEU][hapmap]
rs882010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295690	0.81[CEU][hapmap]
rs9467759	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4713001	BTN2A2	cis	multi-tissue	Pritchard
rs4713001	BTN2A1	cis	parietal	SCAN
rs4713001	ZFYVE9	trans	parietal	SCAN
rs4713001	GMNN	cis	parietal	SCAN
rs4713001	OR4K14	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26476600-26489200	Weak transcription	Stomach Mucosa	stomach
2	chr6:26486000-26488000	Weak transcription	Small Intestine	intestine
3	chr6:26486000-26489600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:26486400-26489400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:26487000-26487600	Weak transcription	Liver	Liver
6	chr6:26487000-26489400	Weak transcription	K562	blood

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