Variant report

Variant	rs6685289
Chromosome Location	chr1:209530669-209530670
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209530006..209531801-chr1:209588176..209590089,2	MCF-7	breast:
2	chr1:209530066..209531138-chr1:209608742..209609668,4	MCF-7	breast:
3	chr1:209524634..209532045-chr1:209599866..209610404,18	MCF-7	breast:
4	chr1:209528146..209530754-chr1:209539138..209540797,2	MCF-7	breast:
5	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:
6	chr1:209530299..209531126-chr1:209608808..209609706,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1014817	0.80[AFR][1000 genomes]
rs1021993	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1027821	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1027823	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10494922	0.82[AFR][1000 genomes]
rs10494924	0.89[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1354854	0.87[EUR][1000 genomes]
rs1395751	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1507341	0.89[EUR][1000 genomes]
rs2055698	0.82[ASN][1000 genomes]
rs2356722	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs2660636	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2660640	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2660642	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2660643	0.89[EUR][1000 genomes]
rs2843168	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661759	0.89[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6674103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674309	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs906347	0.89[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906348	0.88[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs906349	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906350	0.89[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906351	0.89[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs925077	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs937874	0.90[EUR][1000 genomes]
rs950890	0.83[AMR][1000 genomes];0.89[EUR][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	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
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:209527000-209530800	Enhancers	HMEC	breast
3	chr1:209527200-209531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:209527400-209530800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:209527400-209530800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:209527400-209530800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr1:209527600-209530800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:209527600-209530800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:209527600-209530800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:209527600-209531000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:209528200-209530800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:209528400-209536200	Weak transcription	Esophagus	oesophagus
13	chr1:209528400-209536400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:209529000-209531000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr1:209529200-209530800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:209529400-209531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:209529800-209530800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:209529800-209533400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:209529800-209547000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:209530000-209530800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:209530200-209530800	Enhancers	HSMMtube	muscle
22	chr1:209530200-209536000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:209530400-209531000	Enhancers	NHEK	skin
24	chr1:209530400-209536000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:209530600-209530800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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