Variant report

Variant	rs17058990
Chromosome Location	chr13:39596403-39596404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:39596281-39596844	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr13:39595475-39597349	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:39586473..39588132-chr13:39595718..39598014,2	K562	blood:
2	chr13:39594384..39596658-chr13:39611606..39613910,2	MCF-7	breast:
3	chr13:39583306..39585732-chr13:39594165..39596602,2	K562	blood:
4	chr13:39595559..39597525-chr13:39598981..39600626,2	K562	blood:
5	chr13:39595128..39597127-chr13:39603332..39605869,2	K562	blood:
6	chr13:39594195..39597127-chr13:39600978..39605869,5	K562	blood:
7	chr13:39585404..39588263-chr13:39595787..39598231,3	K562	blood:

No data

Variant related genes	Relation type
PROSER1	TF binding region
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11147745	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12428445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12429324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12429338	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12430450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12431316	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1326405	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17058947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17059014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2094252	0.95[ASN][1000 genomes]
rs2094253	0.95[ASN][1000 genomes]
rs2094254	0.95[ASN][1000 genomes]
rs2104518	0.95[ASN][1000 genomes]
rs2274384	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2274385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34316151	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34327528	0.95[ASN][1000 genomes]
rs35804724	1.00[ASN][1000 genomes]
rs35864330	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3751378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3751379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4142398	0.90[ASN][1000 genomes]
rs55809136	1.00[ASN][1000 genomes]
rs66496062	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66908302	0.94[ASN][1000 genomes]
rs67296293	0.94[ASN][1000 genomes]
rs73169457	0.95[ASN][1000 genomes]
rs7317852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7318688	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs747752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7987207	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs7994530	0.92[ASN][1000 genomes]
rs7997052	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs7998475	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8000929	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9566385	0.83[ASN][1000 genomes]
rs9566389	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9566391	1.00[ASN][1000 genomes]
rs9566393	0.90[ASN][1000 genomes]
rs9566396	0.90[ASN][1000 genomes]
rs9566397	0.82[ASN][1000 genomes]
rs9576669	0.87[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs9576670	0.94[ASN][1000 genomes]
rs9576673	0.92[ASN][1000 genomes]
rs9576674	0.94[ASN][1000 genomes]
rs9576676	0.94[ASN][1000 genomes]
rs9576677	0.94[ASN][1000 genomes]
rs9576678	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9576679	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576681	0.95[ASN][1000 genomes]
rs9576683	0.95[ASN][1000 genomes]
rs9576684	0.95[ASN][1000 genomes]
rs9576685	0.95[ASN][1000 genomes]
rs9576686	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576688	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576690	0.94[ASN][1000 genomes]
rs9576692	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576693	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576695	0.95[ASN][1000 genomes]
rs9576696	0.96[ASN][1000 genomes]
rs9576697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576701	1.00[ASN][1000 genomes]
rs9576703	0.98[ASN][1000 genomes]
rs9576705	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9576707	1.00[ASN][1000 genomes]
rs9576710	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576711	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9576717	0.90[ASN][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17058990	LHFP	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr13:39583600-39597200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:39584000-39597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:39584600-39597600	Weak transcription	Fetal Heart	heart
11	chr13:39584600-39603600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr13:39587800-39608200	Weak transcription	Fetal Brain Male	brain
13	chr13:39588400-39597000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:39588400-39608800	Weak transcription	Stomach Mucosa	stomach
15	chr13:39588600-39597800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:39588600-39598800	Weak transcription	Brain Angular Gyrus	brain
17	chr13:39588600-39608200	Weak transcription	Hela-S3	cervix
18	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:39589200-39597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:39589200-39598000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:39589200-39608400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr13:39589200-39609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:39589400-39597600	Weak transcription	Spleen	Spleen
24	chr13:39589600-39597200	Weak transcription	Small Intestine	intestine
25	chr13:39591200-39599400	Weak transcription	Lung	lung
26	chr13:39591200-39599400	Weak transcription	NHLF	lung
27	chr13:39591200-39608400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:39591600-39597800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr13:39591600-39600000	Strong transcription	Fetal Lung	lung
30	chr13:39592200-39602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:39592400-39597600	Weak transcription	Ovary	ovary
32	chr13:39592400-39597800	Weak transcription	Gastric	stomach
33	chr13:39592400-39597800	Weak transcription	Right Ventricle	heart
34	chr13:39592400-39598800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:39592400-39606600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr13:39592600-39597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr13:39592600-39597600	Weak transcription	Aorta	Aorta
38	chr13:39592600-39597800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr13:39592600-39598800	Weak transcription	Fetal Stomach	stomach
40	chr13:39592600-39599400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr13:39592600-39599400	Weak transcription	Esophagus	oesophagus
42	chr13:39592800-39597400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:39593800-39597000	Weak transcription	Fetal Intestine Small	intestine
44	chr13:39594200-39597200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:39594200-39603000	Strong transcription	Adipose Nuclei	Adipose
46	chr13:39594200-39604000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:39594200-39605600	Strong transcription	Dnd41	blood
48	chr13:39594400-39597200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr13:39594400-39597800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:39594400-39604200	Strong transcription	HUVEC	blood vessel

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