Variant report

Variant	rs2820579
Chromosome Location	chr1:159919986-159919987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:159914087..159917406-chr1:159919502..159922854,5	K562	blood:
2	chr1:159906196..159907844-chr1:159918689..159920496,2	K562	blood:
3	chr1:159914087..159917108-chr1:159918737..159921842,4	K562	blood:
4	chr1:159912050..159914185-chr1:159918859..159921422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11591079	1.00[CHB][hapmap]
rs1320570	1.00[CHB][hapmap]
rs17427209	1.00[CHB][hapmap]
rs17467492	1.00[CHB][hapmap]
rs2789415	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789416	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789417	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789420	0.82[AFR][1000 genomes]
rs2820584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2840581	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840583	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2840586	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2840588	1.00[CHB][hapmap]
rs3001288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4297288	1.00[CEU][hapmap]
rs4402127	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662675	1.00[CHB][hapmap]
rs6662918	1.00[CHB][hapmap]

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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr1:159916200-159920000	Enhancers	Stomach Mucosa	stomach
2	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
3	chr1:159916600-159920800	Weak transcription	Fetal Lung	lung
4	chr1:159916800-159923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:159917000-159923400	Weak transcription	NHEK	skin
6	chr1:159918600-159920000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:159918600-159920000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr1:159918600-159920400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:159918600-159921400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:159919000-159920000	Enhancers	Fetal Stomach	stomach
11	chr1:159919200-159920200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:159919400-159923600	Weak transcription	K562	blood
13	chr1:159919600-159920400	Enhancers	Colonic Mucosa	Colon
14	chr1:159919600-159923000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:159919600-159923400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:159919800-159920000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:159919800-159920000	Enhancers	Gastric	stomach
18	chr1:159919800-159920200	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:159919800-159920600	Weak transcription	Lung	lung
20	chr1:159919800-159923600	Weak transcription	Esophagus	oesophagus
21	chr1:159919800-159923800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum

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