Variant report

Variant	rs2968013
Chromosome Location	chr5:58296326-58296327
allele	C/G
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	TCF12	chr5:58295385-58296525	A549	lung:	n/a	n/a
2	SP1	chr5:58295422-58296348	A549	lung:	n/a	chr5:58295850-58295860 chr5:58295850-58295860
3	POLR2A	chr5:58296239-58296457	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:58295501-58296479	A549	lung:	n/a	n/a
5	POLR2A	chr5:58295775-58296332	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10074854	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10461657	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1463816	0.92[EUR][1000 genomes]
rs1498612	0.89[EUR][1000 genomes]
rs1532520	0.89[EUR][1000 genomes]
rs1553114	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs159724	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1846369	0.89[EUR][1000 genomes]
rs1973450	0.90[EUR][1000 genomes]
rs1973451	0.90[EUR][1000 genomes]
rs2409614	0.81[EUR][1000 genomes]
rs2927661	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936190	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936192	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2936193	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2936199	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968006	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968014	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2968015	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968017	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968021	0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805553	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3805554	0.91[EUR][1000 genomes]
rs3805556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805557	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs412423	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4321723	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs457959	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4621516	0.88[EUR][1000 genomes]
rs4629551	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699930	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699931	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700314	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450496	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs6875727	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs702519	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702523	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7712725	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs7713069	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7713345	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs7724713	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs7737685	0.93[CEU][hapmap];0.91[EUR][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:58278400-58297400	Weak transcription	HSMMtube	muscle
4	chr5:58278400-58299000	Weak transcription	Gastric	stomach
5	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
6	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
8	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:58280200-58297000	Weak transcription	Fetal Heart	heart
10	chr5:58280200-58297000	Weak transcription	Fetal Kidney	kidney
11	chr5:58280200-58297200	Weak transcription	Psoas Muscle	Psoas
12	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
13	chr5:58280400-58297600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:58281800-58321600	Weak transcription	Osteobl	bone
15	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:58284400-58297600	Weak transcription	Fetal Lung	lung
17	chr5:58284400-58299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:58286200-58297000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:58286200-58298400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:58286200-58312800	Weak transcription	Lung	lung
21	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
24	chr5:58286600-58297400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:58286600-58298200	Weak transcription	Left Ventricle	heart
26	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
28	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:58287000-58298200	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:58287200-58297400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:58287200-58298400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:58287400-58301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:58287600-58297000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:58288800-58297400	Weak transcription	Hela-S3	cervix
35	chr5:58288800-58297600	Weak transcription	HSMM	muscle
36	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:58289400-58301800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:58289600-58301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:58290200-58299000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:58290600-58297000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr5:58291200-58297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:58293400-58305200	Enhancers	Primary T cells from cord blood	blood
43	chr5:58293600-58297600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr5:58293800-58297600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr5:58294400-58296400	Active TSS	Brain Substantia Nigra	brain
46	chr5:58294800-58299800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:58295400-58296400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:58295400-58303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:58295600-58296400	Enhancers	Rectal Smooth Muscle	rectum
50	chr5:58295600-58297600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links