Variant report

Variant	rs6699699
Chromosome Location	chr1:86063484-86063485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NANOG	chr1:86063482-86063654	H1-hESC	embryonic stem cell:	n/a	chr1:86063565-86063574

No.	Distal block	Cell Line	Cell type
1	chr1:86043937..86050216-chr1:86058297..86066765,12	K562	blood:
2	chr1:86046008..86048463-chr1:86063364..86065472,5	MCF-7	breast:
3	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
4	chr1:86061667..86064228-chr1:86064478..86067432,2	K562	blood:
5	chr1:86046314..86048061-chr1:86063099..86064769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230285	TF binding region
ENSG00000230285	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12756618	0.84[EUR][1000 genomes]
rs17127949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34201212	1.00[EUR][1000 genomes]
rs35003186	1.00[EUR][1000 genomes]
rs35587534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35754509	1.00[EUR][1000 genomes]
rs35787923	1.00[EUR][1000 genomes]
rs36003479	1.00[EUR][1000 genomes]
rs6684769	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs71502515	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7512713	1.00[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7517469	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518036	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527678	0.88[AFR][1000 genomes]
rs7550753	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
3	chr1:86053800-86064600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:86053800-86071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:86055000-86064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:86055200-86064600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:86062400-86064200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:86062400-86064400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
9	chr1:86062600-86063800	Enhancers	Stomach Smooth Muscle	stomach
10	chr1:86062600-86064000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:86062600-86064000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:86062600-86064200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:86062600-86065200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:86062800-86064400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr1:86062800-86065000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:86063000-86063600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:86063000-86063800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:86063000-86063800	Weak transcription	A549	lung
19	chr1:86063000-86064000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:86063000-86064800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:86063000-86069400	Weak transcription	Fetal Lung	lung
22	chr1:86063400-86063600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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