Variant report

Variant	rs2597164
Chromosome Location	chr17:46069980-46069981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46068180..46070484-chr17:46078345..46080253,2	K562	blood:
2	chr17:46067363..46070212-chr17:46079475..46083776,4	MCF-7	breast:
3	chr17:46058631..46063478-chr17:46064617..46070061,8	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11079800	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs2255814	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256020	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525097	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2525104	0.86[EUR][1000 genomes]
rs2597177	0.87[CHB][hapmap]
rs2597178	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826396	0.82[EUR][1000 genomes]
rs4794331	0.91[CEU][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs57768342	0.82[EUR][1000 genomes]
rs7216411	0.84[ASW][hapmap];0.87[CHB][hapmap]
rs736387	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[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2597164	ATP6V0A1	cis	parietal	SCAN
rs2597164	VAT1	cis	cerebellum	SCAN
rs2597164	NFE2L1	cis	cerebellum	SCAN
rs2597164	SP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
2	chr17:46063400-46074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:46063600-46074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:46064200-46071000	Enhancers	HSMMtube	muscle
5	chr17:46064800-46071400	Weak transcription	Pancreas	Pancrea
6	chr17:46065400-46072600	Weak transcription	Fetal Lung	lung
7	chr17:46066400-46072600	Weak transcription	Spleen	Spleen
8	chr17:46068000-46070000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:46068000-46070800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:46068000-46074200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr17:46068200-46071000	Enhancers	Fetal Brain Female	brain
13	chr17:46068200-46074200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:46068400-46070000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46068400-46073000	Weak transcription	Fetal Kidney	kidney
16	chr17:46068600-46070000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr17:46069000-46070200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr17:46069000-46071600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr17:46069000-46071600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:46069000-46072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:46069000-46072600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:46069000-46077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:46069000-46079600	Weak transcription	Fetal Thymus	thymus
24	chr17:46069200-46070000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr17:46069200-46070000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr17:46069200-46070000	Bivalent Enhancer	HepG2	liver
27	chr17:46069200-46070600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr17:46069200-46072000	Weak transcription	Brain Germinal Matrix	brain
29	chr17:46069200-46072000	Weak transcription	Fetal Brain Male	brain
30	chr17:46069200-46074400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:46069400-46070000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr17:46069400-46072000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr17:46069400-46072000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:46069400-46072600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:46069400-46072600	Weak transcription	Fetal Muscle Leg	muscle
36	chr17:46069600-46070000	Enhancers	Left Ventricle	heart
37	chr17:46069600-46070000	Enhancers	K562	blood
38	chr17:46069600-46070800	Enhancers	Right Ventricle	heart
39	chr17:46069600-46071800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr17:46069800-46070000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr17:46069800-46070000	Bivalent Enhancer	Fetal Heart	heart
42	chr17:46069800-46071600	Weak transcription	Placenta	Placenta
43	chr17:46069800-46071800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:46069800-46074400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:46069800-46075000	Weak transcription	HSMM	muscle

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