Variant report

Variant	rs6971826
Chromosome Location	chr7:33569954-33569955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:33568845..33571734-chr7:33576491..33579149,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10282539	0.81[JPT][hapmap];0.84[YRI][hapmap]
rs1882039	0.81[JPT][hapmap]
rs2392246	0.92[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2392247	0.81[JPT][hapmap]
rs2392248	0.85[JPT][hapmap]
rs4720121	0.82[JPT][hapmap]
rs6462484	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6945776	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6951439	0.83[LWK][hapmap]
rs6957890	0.81[JPT][hapmap]
rs6974597	0.81[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap]
rs969402	0.89[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933237	chr7:33470390-33574046	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv933018	chr7:33506325-33707270	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv830945	chr7:33526648-33670592	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6971826	PM20D1	trans	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33542400-33574200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:33543600-33574200	Weak transcription	Ovary	ovary
3	chr7:33547000-33579400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:33557200-33572600	Weak transcription	Aorta	Aorta
5	chr7:33557200-33572800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:33560400-33570800	Weak transcription	Lung	lung
7	chr7:33567400-33573600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:33567600-33574200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:33567600-33578800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:33568000-33572800	Weak transcription	Fetal Intestine Large	intestine
11	chr7:33568800-33573000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:33568800-33574200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:33568800-33574400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:33568800-33574800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:33569000-33572800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:33569000-33574200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:33569000-33574200	Weak transcription	Left Ventricle	heart
18	chr7:33569000-33576800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:33569000-33580400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:33569000-33584000	Weak transcription	Right Ventricle	heart
21	chr7:33569200-33574600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:33569600-33572800	Weak transcription	Primary T cells from cord blood	blood

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