Variant report

Variant	rs17825846
Chromosome Location	chr14:65598752-65598753
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65568387..65571112-chr14:65596927..65600047,3	MCF-7	breast:
2	chr14:65595405..65599836-chr14:65877134..65881265,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125952	Chromatin interaction
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10873180	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10873181	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10873182	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10873183	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10873185	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11158572	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158573	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158574	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158577	0.83[CHB][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs11158578	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11625045	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs11626156	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11626496	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11627859	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12147959	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12880781	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12884836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12887607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888794	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17102423	0.84[EUR][1000 genomes]
rs1953228	0.95[ASN][1000 genomes]
rs2898863	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34062462	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35002541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35176994	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769504	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45604339	0.83[ASN][1000 genomes]
rs4899161	0.83[CEU][hapmap]
rs4902358	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs4902361	0.83[CEU][hapmap]
rs4902364	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902365	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902367	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55658675	0.95[ASN][1000 genomes]
rs61987428	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61987429	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7143495	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7144259	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7154852	0.95[ASN][1000 genomes]
rs7156617	0.83[CEU][hapmap]
rs7161394	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs762810	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs8004805	0.83[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs8009396	0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8009714	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015330	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8181937	0.95[ASN][1000 genomes]
rs8181938	0.95[ASN][1000 genomes]
rs8181939	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs868814	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884683	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942627	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][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	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	esv1833060	chr14:65594460-65607642	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17825846	CHURC1	cis	multi-tissue	Pritchard
rs17825846	MAX	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65596800-65602600	Enhancers	Fetal Intestine Small	intestine
2	chr14:65597800-65598800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr14:65597800-65598800	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr14:65597800-65599000	Enhancers	NHEK	skin
5	chr14:65597800-65602600	Enhancers	Fetal Intestine Large	intestine
6	chr14:65598000-65598800	Enhancers	HMEC	breast
7	chr14:65598200-65601400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:65598200-65601600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:65598200-65602200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr14:65598400-65601400	Weak transcription	HSMM	muscle
11	chr14:65598600-65598800	Enhancers	Colonic Mucosa	Colon
12	chr14:65598600-65598800	Enhancers	Osteobl	bone

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