Variant report

Variant	rs2970555
Chromosome Location	chr1:209376550-209376551
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	chr1:209375950..209376832-chr1:209421724..209422654,5	MCF-7	breast:
2	chr1:209376128..209379505-chr1:209382757..209384972,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11586407	0.82[ASN][1000 genomes]
rs11586451	0.84[ASN][1000 genomes]
rs12722814	0.82[ASN][1000 genomes]
rs12755287	0.82[ASN][1000 genomes]
rs1933612	0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs1933619	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs2266024	0.84[EUR][1000 genomes]
rs2489651	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788152	0.83[CEU][hapmap]
rs2788158	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788159	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788161	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788162	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788168	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788170	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970556	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970560	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996683	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996687	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2996688	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523921	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944110	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396124	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4402132	0.84[ASN][1000 genomes]
rs6658956	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6672407	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs66763810	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678963	0.82[ASN][1000 genomes]
rs6692414	0.84[ASN][1000 genomes]
rs6704132	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs71636106	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2970555	NUCKS1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209373600-209376600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:209373600-209376600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:209373600-209380400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:209373800-209376600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:209373800-209376600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:209375600-209376600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:209375600-209377600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:209376200-209376800	Enhancers	Fetal Stomach	stomach
12	chr1:209376200-209377000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:209376200-209377000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:209376200-209378200	Enhancers	Fetal Brain Female	brain
15	chr1:209376200-209378800	Enhancers	Fetal Brain Male	brain
16	chr1:209376400-209376600	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:209376400-209376600	Enhancers	Fetal Intestine Small	intestine
18	chr1:209376400-209376600	Enhancers	Hela-S3	cervix
19	chr1:209376400-209376800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:209376400-209376800	Enhancers	Colon Smooth Muscle	Colon
21	chr1:209376400-209377000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:209376400-209377000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:209376400-209377000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:209376400-209377000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr1:209376400-209377200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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