Variant report

Variant	rs7254170
Chromosome Location	chr19:38123793-38123794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38115350..38117839-chr19:38123241..38125691,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1038084	0.84[CEU][hapmap]
rs1038085	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407657	0.84[CEU][hapmap]
rs10417204	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10424612	0.84[CEU][hapmap]
rs10425671	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665877	0.87[EUR][1000 genomes]
rs11667454	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667457	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11668558	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs11670655	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672077	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883392	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1236810	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12972712	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12981237	0.87[EUR][1000 genomes]
rs12982288	0.88[EUR][1000 genomes]
rs12983298	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17306508	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17306795	1.00[CHB][hapmap]
rs1871197	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045909	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126978	0.83[CEU][hapmap]
rs2160640	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199644	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291000	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385116	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385124	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385125	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241937	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs241940	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.83[AFR][1000 genomes]
rs241941	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241942	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.83[AFR][1000 genomes]
rs241946	0.83[AFR][1000 genomes]
rs241947	0.84[EUR][1000 genomes]
rs241948	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs241951	1.00[CHB][hapmap]
rs241953	0.83[EUR][1000 genomes]
rs2617789	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2909106	0.82[EUR][1000 genomes]
rs2927741	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927744	0.84[CEU][hapmap]
rs2972453	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972454	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972456	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972459	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112435	0.88[EUR][1000 genomes]
rs34351186	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607899	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34782935	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34949193	0.83[EUR][1000 genomes]
rs35015599	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35214625	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35273320	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35415221	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36020184	0.87[EUR][1000 genomes]
rs36092052	0.87[EUR][1000 genomes]
rs3752365	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4273159	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482404	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4802066	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802069	0.84[CEU][hapmap]
rs4803216	0.84[CEU][hapmap]
rs4803228	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57308437	0.88[EUR][1000 genomes]
rs62108304	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108339	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62108355	0.86[EUR][1000 genomes]
rs6508729	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6508738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251097	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs7253174	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254828	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7255283	0.84[CEU][hapmap]
rs8111055	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8113076	0.84[CEU][hapmap]
rs856302	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7254170	RABAC1	cis	cerebellum	SCAN
rs7254170	CEACAM16	cis	parietal	SCAN
rs7254170	CD3EAP	cis	cerebellum	SCAN
rs7254170	ITPKC	cis	cerebellum	SCAN
rs7254170	ARHGEF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38121800-38139200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:38121800-38140600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38122200-38125000	Weak transcription	HSMM	muscle
4	chr19:38122400-38124800	Weak transcription	HSMMtube	muscle
5	chr19:38123000-38126000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:38123200-38125800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:38123400-38138800	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:38123600-38130400	ZNF genes & repeats	Brain Germinal Matrix	brain
9	chr19:38123600-38133600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:38123600-38140000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:38123600-38140800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:38123600-38141400	ZNF genes & repeats	Liver	Liver

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