Variant report

Variant	rs5998329
Chromosome Location	chr22:32633785-32633786
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	22:32633450-32636825..22:32740683-32750950	H1-hESC	embryonic stem cell:	embryo
2	22:32633450-32636825..22:33452523-33459358	Hela-S3	cervix:
3	22:32633450-32636825..22:32750950-32761732	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000205853	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000128276	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12157791	1.00[JPT][hapmap]
rs12160790	1.00[JPT][hapmap]
rs136489	0.81[CEU][hapmap]
rs16990065	1.00[JPT][hapmap]
rs16990066	1.00[JPT][hapmap]
rs2068209	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2142558	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2142559	1.00[CHB][hapmap]
rs2179065	1.00[CHB][hapmap]
rs2179066	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235168	1.00[JPT][hapmap]
rs2235171	0.89[JPT][hapmap]
rs2294205	0.94[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294206	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294207	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2294211	0.89[JPT][hapmap]
rs34663221	0.84[EUR][1000 genomes]
rs5994491	1.00[JPT][hapmap]
rs5994496	1.00[JPT][hapmap]
rs5994502	1.00[JPT][hapmap]
rs5994503	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5994511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5994512	1.00[JPT][hapmap]
rs5998300	1.00[JPT][hapmap]
rs5998317	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5998318	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5998321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5998323	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998326	1.00[JPT][hapmap]
rs5998328	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998330	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7287853	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7289226	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7291681	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7292721	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs734023	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8137034	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9606920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv834178	chr22:32490449-32677521	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv2753006	chr22:32592120-32719481	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5998329	BCAR1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32623800-32633800	Weak transcription	Fetal Intestine Small	intestine
2	chr22:32628600-32634800	Weak transcription	Spleen	Spleen
3	chr22:32629400-32636600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr22:32629600-32640800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr22:32632600-32634200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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