Variant report

Variant	rs4346460
Chromosome Location	chr20:23569400-23569401
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	chr20:23562870..23565685-chr20:23566645..23569407,3	K562	blood:
2	chr20:23568486..23570139-chr9:92478980..92480480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204658	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1010117	0.81[EUR][1000 genomes]
rs1011226	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1158167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12624424	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625182	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625716	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12710327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13037490	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13038305	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs13038337	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13038990	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13039536	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs13043266	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13043610	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1555355	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17751897	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2067488	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2208289	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254635	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs2405367	0.81[CEU][hapmap]
rs2405392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424582	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs28703706	0.85[EUR][1000 genomes]
rs3004139	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3004145	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088162	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs34374560	0.81[EUR][1000 genomes]
rs34792920	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34911568	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35573837	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35610040	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs35782710	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787498	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs3787499	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs3810575	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827141	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs3827142	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs3827143	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs4815222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815223	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815224	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897275	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56077567	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56371840	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56388902	0.89[EUR][1000 genomes]
rs57549987	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59059917	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036463	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036465	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036469	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036470	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036471	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036474	0.85[EUR][1000 genomes]
rs6036476	0.81[EUR][1000 genomes]
rs6036478	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6048920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048923	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048924	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048925	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048928	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048929	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048930	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6048933	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048936	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048939	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6048941	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6048945	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048946	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6048950	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048952	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6048956	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs61035931	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6106685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114201	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs6114206	0.81[EUR][1000 genomes]
rs6114208	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs6515375	0.80[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs67997662	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7265178	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7270413	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8114619	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8115417	0.85[EUR][1000 genomes]
rs8115423	0.85[EUR][1000 genomes]
rs8116859	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8121147	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8121283	0.85[EUR][1000 genomes]
rs8121405	0.85[EUR][1000 genomes]
rs911119	0.90[CEU][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4346460	CST3	cis	cerebellum	SCAN
rs4346460	GINS1	cis	parietal	SCAN
rs4346460	CST3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23568000-23569400	Weak transcription	NHEK	skin
2	chr20:23568200-23569600	Weak transcription	HMEC	breast
3	chr20:23568400-23569400	Weak transcription	Fetal Intestine Small	intestine
4	chr20:23568400-23570000	Enhancers	HepG2	liver
5	chr20:23568600-23569600	Weak transcription	Placenta	Placenta
6	chr20:23569000-23569800	Enhancers	Stomach Mucosa	stomach
7	chr20:23569200-23569400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr20:23569200-23569600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:23569200-23569600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr20:23569200-23569600	Enhancers	K562	blood
11	chr20:23569200-23569800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr20:23569200-23569800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:23569200-23570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:23569200-23570000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:23569200-23570000	Enhancers	Fetal Thymus	thymus
16	chr20:23569400-23569600	Enhancers	Fetal Intestine Small	intestine
17	chr20:23569400-23569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr20:23569400-23569800	Enhancers	Adipose Nuclei	Adipose
19	chr20:23569400-23569800	Enhancers	NHEK	skin

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