Variant report

Variant	rs12564961
Chromosome Location	chr1:57573514-57573515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57571162..57573727-chr1:57574083..57575763,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11206975	1.00[CEU][hapmap]
rs11206981	1.00[CEU][hapmap]
rs12405609	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12406184	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12407883	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12408256	1.00[CEU][hapmap]
rs12562392	1.00[CEU][hapmap]
rs12562394	1.00[CEU][hapmap]
rs12562609	1.00[CEU][hapmap]
rs12562930	1.00[CEU][hapmap]
rs12563280	1.00[CEU][hapmap]
rs12564278	1.00[CEU][hapmap]
rs12566131	1.00[CEU][hapmap]
rs12566320	1.00[CEU][hapmap]
rs12567335	1.00[CEU][hapmap]
rs12567531	1.00[CEU][hapmap]
rs12567904	1.00[CEU][hapmap]
rs12568148	1.00[CEU][hapmap]
rs12568862	1.00[CEU][hapmap]
rs17114840	1.00[JPT][hapmap]
rs17114978	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17115105	1.00[CEU][hapmap]
rs17115108	1.00[CEU][hapmap]
rs17115146	1.00[CEU][hapmap]
rs17115155	1.00[CEU][hapmap]
rs17115222	1.00[CEU][hapmap]
rs17115397	1.00[CEU][hapmap]
rs17115580	1.00[CEU][hapmap]
rs17115587	1.00[CEU][hapmap]
rs17419873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17420013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17420181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17420216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17421219	1.00[CEU][hapmap]
rs17421839	1.00[CEU][hapmap]
rs17422039	1.00[CEU][hapmap]
rs17453874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455073	1.00[CEU][hapmap]
rs17455469	1.00[CEU][hapmap]
rs17455616	1.00[CEU][hapmap]
rs17455728	1.00[CEU][hapmap]
rs17455840	1.00[CEU][hapmap]
rs35522019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55706301	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61765294	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765295	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765320	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6697173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs728719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12564961	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57567400-57576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57569200-57574200	Weak transcription	Right Atrium	heart
4	chr1:57569400-57573600	Weak transcription	Ovary	ovary
5	chr1:57569400-57574400	Weak transcription	Left Ventricle	heart
6	chr1:57570800-57574200	Weak transcription	Fetal Heart	heart
7	chr1:57571600-57575600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:57571600-57577600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:57571800-57575600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:57571800-57577000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:57572000-57576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:57572200-57576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:57572200-57577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:57573400-57574400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:57573400-57577400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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