Variant report

Variant	rs6724477
Chromosome Location	chr2:99537074-99537075
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99496861..99499359-chr2:99536872..99539467,2	K562	blood:
2	chr2:99536889..99540003-chr2:99549553..99553689,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10192266	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123756	0.81[EUR][1000 genomes]
rs11900176	0.81[TSI][hapmap]
rs12474283	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs12478574	0.81[EUR][1000 genomes]
rs12712037	0.81[TSI][hapmap]
rs12712040	0.81[EUR][1000 genomes]
rs12712041	0.83[AMR][1000 genomes]
rs12712042	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712043	0.83[AMR][1000 genomes]
rs13004700	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs13005124	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13006398	0.83[EUR][1000 genomes]
rs13011428	0.83[AMR][1000 genomes]
rs13024838	0.87[EUR][1000 genomes]
rs13025913	0.81[AMR][1000 genomes]
rs13028500	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1607256	0.83[AMR][1000 genomes]
rs17758170	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1878589	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1949424	0.84[EUR][1000 genomes]
rs1962029	0.81[EUR][1000 genomes]
rs1976766	0.81[AMR][1000 genomes]
rs1983352	0.81[GIH][hapmap]
rs2048949	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4311103	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4499468	0.81[EUR][1000 genomes]
rs4553869	0.81[EUR][1000 genomes]
rs4850889	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4850890	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4851173	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4851174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851175	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851176	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851177	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6419564	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6542841	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6542843	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6542845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704682	0.81[EUR][1000 genomes]
rs6739176	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6739503	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6741166	0.87[EUR][1000 genomes]
rs6742047	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752025	0.85[EUR][1000 genomes]
rs6757098	0.96[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6760065	0.96[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7423519	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7565510	0.81[EUR][1000 genomes]
rs7565819	0.87[EUR][1000 genomes]
rs7588441	0.87[EUR][1000 genomes]
rs7593332	0.84[EUR][1000 genomes]
rs7608889	0.81[CEU][hapmap]
rs883773	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs908672	0.86[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925887	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6724477	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6724477	LIPT1	cis	cerebellum	SCAN
rs6724477	LIPT1	cis	parietal	SCAN
rs6724477	TSGA10	cis	cerebellum	SCAN
rs6724477	TSGA10	cis	multi-tissue	Pritchard
rs6724477	TBC1D8	cis	parietal	SCAN
rs6724477	UNC50	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99531200-99539000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99532000-99537400	Weak transcription	Gastric	stomach
3	chr2:99532400-99542800	Weak transcription	Pancreas	Pancrea
4	chr2:99534200-99539000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:99534400-99537400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:99536200-99538400	Enhancers	HMEC	breast
7	chr2:99536800-99538200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:99536800-99538400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:99536800-99538400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:99536800-99538400	Enhancers	Esophagus	oesophagus
11	chr2:99536800-99539200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:99537000-99538400	Enhancers	NHEK	skin

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