Variant report

Variant	rs925887
Chromosome Location	chr2:99514671-99514672
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99511094..99513536-chr2:99513971..99515914,2	MCF-7	breast:
2	chr2:99513625..99516129-chr2:99517702..99519435,2	K562	blood:
3	chr2:99514144..99517054-chr2:99525112..99527785,2	MCF-7	breast:
4	chr2:99224479..99226496-chr2:99514004..99516760,2	MCF-7	breast:
5	chr2:99505531..99508517-chr2:99513277..99515165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10169003	0.87[EUR][1000 genomes]
rs10172158	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178956	0.84[ASN][1000 genomes]
rs10181972	0.87[EUR][1000 genomes]
rs10188156	0.80[EUR][1000 genomes]
rs10192266	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11123755	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11887536	0.84[EUR][1000 genomes]
rs11893888	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12468024	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12474283	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712038	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712039	0.82[EUR][1000 genomes]
rs12712041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712042	0.83[AMR][1000 genomes]
rs12712043	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13004700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004923	0.87[EUR][1000 genomes]
rs13005124	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13011428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025076	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13025913	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13028500	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1581250	0.87[EUR][1000 genomes]
rs1581251	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1607256	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17758170	0.92[CEU][hapmap]
rs1878585	0.87[EUR][1000 genomes]
rs1878589	0.92[CEU][hapmap]
rs1976766	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983352	0.84[GIH][hapmap];0.80[TSI][hapmap]
rs4263159	0.80[EUR][1000 genomes]
rs4311103	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4850889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4850890	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4851162	0.80[EUR][1000 genomes]
rs4851163	0.80[EUR][1000 genomes]
rs4851167	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851170	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851171	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851174	0.86[CEU][hapmap];0.85[AMR][1000 genomes]
rs4851175	0.86[CEU][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4851176	0.81[AMR][1000 genomes]
rs4851177	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56125264	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419564	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6542838	0.80[EUR][1000 genomes]
rs6542841	0.87[CEU][hapmap]
rs6542843	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6542845	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6713991	0.80[EUR][1000 genomes]
rs6714243	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717372	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6724477	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs6739176	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6739503	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742047	0.85[AMR][1000 genomes]
rs6757098	0.87[CEU][hapmap]
rs6760065	0.87[CEU][hapmap]
rs7423519	0.92[CEU][hapmap]
rs7579189	0.80[EUR][1000 genomes]
rs7608889	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883773	0.87[CEU][hapmap]
rs908672	0.92[ASW][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap]
rs981601	0.80[EUR][1000 genomes]
rs981602	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs925887	UNC50	cis	cerebellum	SCAN
rs925887	LIPT1	cis	cerebellum	SCAN
rs925887	TSGA10	cis	parietal	SCAN
rs925887	TSGA10	cis	multi-tissue	Pritchard
rs925887	LIPT1	cis	parietal	SCAN
rs925887	TSGA10	cis	cerebellum	SCAN
rs925887	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs925887	TSGA10	cis	Lymphoblastoid	GTEx
rs925887	FAHD2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99500000-99517000	Weak transcription	Gastric	stomach
2	chr2:99511200-99520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
4	chr2:99513200-99515000	Weak transcription	Pancreas	Pancrea
5	chr2:99513200-99515400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:99513400-99520600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:99513800-99515600	Weak transcription	HSMMtube	muscle
9	chr2:99514600-99515200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:99514600-99515200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:99514600-99515200	Enhancers	Lung	lung

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