Variant report

Variant	rs17421839
Chromosome Location	chr1:57757551-57757552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:57757122-57757648	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:57757172-57757579	H1-neurons	neurons:	n/a	n/a
3	REST	chr1:57757185-57757554	H1-neurons	neurons:	n/a	chr1:57757223-57757237 chr1:57757225-57757233

Variant related genes	Relation type
DAB1	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs11206975	1.00[CEU][hapmap]
rs11206981	1.00[CEU][hapmap]
rs12032549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12408256	1.00[CEU][hapmap]
rs12561986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562555	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12562609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12562847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12563280	1.00[CEU][hapmap]
rs12563894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12564278	1.00[CEU][hapmap]
rs12564961	1.00[CEU][hapmap]
rs12565921	0.92[ASN][1000 genomes]
rs12566131	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12566162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12566320	1.00[CEU][hapmap]
rs12567335	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12567531	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12567904	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567967	1.00[EUR][1000 genomes]
rs12568148	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568708	0.92[ASN][1000 genomes]
rs12568862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568928	1.00[EUR][1000 genomes]
rs12568979	1.00[EUR][1000 genomes]
rs12568992	1.00[JPT][hapmap]
rs12569224	1.00[EUR][1000 genomes]
rs17115023	1.00[CEU][hapmap]
rs17115030	1.00[CEU][hapmap]
rs17115105	1.00[CEU][hapmap]
rs17115108	1.00[CEU][hapmap]
rs17115146	1.00[CEU][hapmap]
rs17115155	1.00[CEU][hapmap]
rs17115222	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17115397	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17115441	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17115445	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17115580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17115587	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17420013	1.00[CEU][hapmap]
rs17420216	1.00[CEU][hapmap]
rs17421219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17422039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17455073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17455469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455616	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17455728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197599	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs197606	1.00[JPT][hapmap]
rs197623	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs59762173	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765330	0.86[EUR][1000 genomes]
rs61765331	0.86[EUR][1000 genomes]
rs61765332	0.86[EUR][1000 genomes]
rs61765561	1.00[EUR][1000 genomes]
rs61765563	1.00[EUR][1000 genomes]
rs61765578	1.00[EUR][1000 genomes]
rs61765580	1.00[EUR][1000 genomes]
rs61765581	1.00[EUR][1000 genomes]
rs61765586	1.00[EUR][1000 genomes]
rs61765589	1.00[EUR][1000 genomes]
rs61765590	1.00[EUR][1000 genomes]
rs61765591	1.00[EUR][1000 genomes]
rs61765592	1.00[EUR][1000 genomes]
rs61765593	1.00[EUR][1000 genomes]
rs61765594	1.00[EUR][1000 genomes]
rs61765595	1.00[EUR][1000 genomes]
rs61765623	1.00[EUR][1000 genomes]
rs61765627	0.88[ASN][1000 genomes]
rs61765630	0.88[ASN][1000 genomes]
rs61765631	0.88[ASN][1000 genomes]
rs61765632	0.88[ASN][1000 genomes]
rs61765653	0.88[ASN][1000 genomes]
rs61765654	0.88[ASN][1000 genomes]
rs61765655	0.88[ASN][1000 genomes]
rs61765656	0.92[ASN][1000 genomes]
rs61765658	0.92[ASN][1000 genomes]
rs61765659	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61767360	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61767361	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61767362	0.97[ASN][1000 genomes]
rs61767363	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767364	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767365	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767387	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61767393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61767394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61767395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61767396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61767398	0.95[ASN][1000 genomes]
rs61767399	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61767400	0.90[ASN][1000 genomes]
rs61767401	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61767411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61767412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61767514	1.00[EUR][1000 genomes]
rs61767515	1.00[EUR][1000 genomes]
rs61767516	1.00[EUR][1000 genomes]
rs61767517	1.00[EUR][1000 genomes]
rs6587766	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6695086	1.00[EUR][1000 genomes]
rs6697173	1.00[CEU][hapmap]
rs728719	1.00[CEU][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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv19252	chr1:57756856-57757610	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57747600-57769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:57751600-57765600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:57751600-57770600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:57753000-57759400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:57756200-57759800	Weak transcription	Fetal Brain Female	brain
6	chr1:57757400-57758400	Weak transcription	Fetal Brain Male	brain

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