Variant report

Variant	rs17598689
Chromosome Location	chr2:63234553-63234554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63232773..63235158-chr2:63276738..63278873,2	K562	blood:
2	chr2:63224659..63226887-chr2:63232348..63235266,2	K562	blood:

Variant related genes	Relation type
ENSG00000115507	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11125949	0.89[GIH][hapmap]
rs12612046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614162	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	1.00[ASW][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17432559	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432566	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs17432580	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432615	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	0.84[EUR][1000 genomes]
rs17598881	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671458	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17598689	AFTPH	cis	cerebellum	SCAN
rs17598689	OTX1	cis	Whole Blood	GTEx
rs17598689	TMEM17	cis	cerebellum	SCAN
rs17598689	PEX13	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
3	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:63197600-63234800	Strong transcription	HepG2	liver
6	chr2:63199800-63258200	Weak transcription	Lung	lung
7	chr2:63200800-63239400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:63205000-63238200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:63207600-63235200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:63207800-63246000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:63207800-63258000	Weak transcription	Placenta	Placenta
12	chr2:63208200-63242600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:63209400-63260000	Weak transcription	Aorta	Aorta
14	chr2:63209600-63239800	Weak transcription	Psoas Muscle	Psoas
15	chr2:63210000-63235400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:63219200-63245600	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:63219200-63269800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:63219400-63261600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:63220200-63250600	Weak transcription	Small Intestine	intestine
20	chr2:63220800-63236200	Weak transcription	Fetal Intestine Small	intestine
21	chr2:63221600-63255600	Weak transcription	Fetal Kidney	kidney
22	chr2:63221800-63245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:63221800-63255200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:63224200-63242000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:63224400-63239800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:63224400-63240400	Weak transcription	Primary T cells from cord blood	blood
27	chr2:63224400-63240400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:63224400-63240600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:63224400-63243800	Weak transcription	Fetal Stomach	stomach
30	chr2:63224400-63248400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:63224400-63251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:63224400-63256200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:63224600-63240600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:63224600-63240600	Weak transcription	Left Ventricle	heart
35	chr2:63224600-63243600	Weak transcription	Fetal Intestine Large	intestine
36	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus
37	chr2:63224600-63272000	Weak transcription	NHLF	lung
38	chr2:63224800-63246200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:63225000-63240400	Weak transcription	Ovary	ovary
40	chr2:63225600-63250000	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:63225800-63250200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:63226000-63240800	Weak transcription	Dnd41	blood
43	chr2:63226400-63235000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:63226800-63239600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:63226800-63243400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:63227400-63240800	Weak transcription	HSMM	muscle
47	chr2:63227400-63243800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:63227400-63244000	Weak transcription	Pancreas	Pancrea
49	chr2:63227400-63258400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:63227400-63259200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links