Variant report

Variant	rs10402308
Chromosome Location	chr19:19657500-19657501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19656094..19658685-chr19:19688090..19690967,2	K562	blood:
2	chr19:19653642..19665886-chr19:19736282..19742268,24	MCF-7	breast:
3	chr19:19656004..19657645-chr19:19659685..19661729,2	K562	blood:
4	chr19:19630106..19632740-chr19:19655430..19658007,2	K562	blood:
5	chr19:19655485..19657839-chr19:19672658..19674603,2	K562	blood:

Variant related genes	Relation type
ENSG00000105717	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1000237	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10282	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs10401193	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402451	0.90[ASN][1000 genomes]
rs10402627	0.91[ASN][1000 genomes]
rs10404728	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10405625	0.85[ASN][1000 genomes]
rs10410664	0.85[ASN][1000 genomes]
rs10414830	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs10419912	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs10422819	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[ASN][1000 genomes]
rs1047361	0.90[ASN][1000 genomes]
rs1054284	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs1054930	0.95[ASN][1000 genomes]
rs1063966	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs11669516	0.92[CHB][hapmap]
rs12972397	0.93[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs12973258	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs12975119	0.85[ASN][1000 genomes]
rs12977524	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs12981405	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465695	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1469712	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1469713	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1808653	0.81[ASN][1000 genomes]
rs1858999	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1865034	0.90[ASN][1000 genomes]
rs2082421	0.81[ASN][1000 genomes]
rs2099333	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2099334	0.85[ASN][1000 genomes]
rs2163804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2163805	0.81[EUR][1000 genomes]
rs2285628	1.00[CEU][hapmap]
rs2288852	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2304098	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[ASN][1000 genomes]
rs2315279	0.82[ASN][1000 genomes]
rs2315281	0.81[ASN][1000 genomes]
rs2315610	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2905431	0.83[ASN][1000 genomes]
rs2916069	0.82[ASN][1000 genomes]
rs2916073	0.85[ASN][1000 genomes]
rs2916074	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs2916076	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2965180	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs2965182	0.85[ASN][1000 genomes]
rs2965183	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2965188	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2965189	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[ASN][1000 genomes]
rs34277109	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs35418933	0.82[ASN][1000 genomes]
rs3752151	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs3794990	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs3794993	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[ASN][1000 genomes]
rs4808198	0.84[ASN][1000 genomes]
rs4808199	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4808200	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs4808202	0.85[ASN][1000 genomes]
rs4808203	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs4808208	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[ASN][1000 genomes]
rs4808955	0.84[ASN][1000 genomes]
rs4808957	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4808959	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4808960	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs4808961	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4808964	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs4808965	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs4808967	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs60003758	0.80[EUR][1000 genomes]
rs6511036	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs6511038	0.88[ASN][1000 genomes]
rs6909	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs7245983	1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs7250658	0.81[EUR][1000 genomes]
rs7250893	0.93[ASN][1000 genomes]
rs7252888	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7253807	0.94[ASN][1000 genomes]
rs7256149	0.84[ASN][1000 genomes]
rs747050	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs751856	0.90[ASN][1000 genomes]
rs751858	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754255	0.83[EUR][1000 genomes]
rs892021	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs892022	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs892023	0.82[MKK][hapmap];0.83[YRI][hapmap]
rs968525	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs9917108	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv543928	chr19:19649839-19664043	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10402308	FAM125A	cis	cerebellum	SCAN
rs10402308	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19652000-19688400	Weak transcription	Right Atrium	heart
3	chr19:19652200-19657600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:19652200-19658000	Weak transcription	Right Ventricle	heart
5	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:19652600-19659000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:19652600-19660800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:19652600-19686200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:19655400-19659200	Bivalent Enhancer	Placenta	Placenta
10	chr19:19655600-19660800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:19656400-19659000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:19657000-19658000	Enhancers	Adipose Nuclei	Adipose
13	chr19:19657000-19661600	Enhancers	Fetal Heart	heart
14	chr19:19657200-19657600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:19657200-19657600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:19657200-19657800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr19:19657200-19658200	Flanking Active TSS	Hela-S3	cervix
18	chr19:19657400-19657600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:19657400-19657600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:19657400-19657600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr19:19657400-19657600	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr19:19657400-19657800	Enhancers	Esophagus	oesophagus
23	chr19:19657400-19657800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr19:19657400-19658000	Enhancers	HMEC	breast
25	chr19:19657400-19658200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:19657400-19659400	Enhancers	Left Ventricle	heart

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