Variant report

Variant	rs2789416
Chromosome Location	chr1:159923628-159923629
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	chr1:159892760..159896965-chr1:159922291..159925141,4	K562	blood:

Variant related genes	Relation type
ENSG00000158710	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2789417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2789418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2789420	0.80[EUR][1000 genomes]
rs2820579	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]
rs2820584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2840581	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2840583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2840586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2840588	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs3001288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4297288	1.00[CEU][hapmap]
rs4402127	1.00[CEU][hapmap];0.86[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	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
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2789416	FAHD2A	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159923800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:159920000-159923800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:159922800-159924000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:159922800-159924200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:159923000-159926200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:159923200-159924200	Enhancers	Stomach Mucosa	stomach
9	chr1:159923200-159924400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:159923200-159924400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:159923200-159924600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:159923400-159924000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:159923400-159924400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:159923400-159926400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:159923400-159926400	Enhancers	NHEK	skin
16	chr1:159923600-159923800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr1:159923600-159924000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:159923600-159924000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:159923600-159924000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
20	chr1:159923600-159924000	Enhancers	Esophagus	oesophagus
21	chr1:159923600-159924000	Bivalent Enhancer	Placenta	Placenta
22	chr1:159923600-159924000	Enhancers	HSMMtube	muscle
23	chr1:159923600-159924400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:159923600-159924400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:159923600-159924400	Enhancers	HSMM	muscle
26	chr1:159923600-159924400	Enhancers	K562	blood
27	chr1:159923600-159924400	Enhancers	Osteobl	bone
28	chr1:159923600-159925400	Enhancers	HMEC	breast
29	chr1:159923600-159925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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