Variant report

Variant	rs713728
Chromosome Location	chr22:29538468-29538469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12157998	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056416	0.95[CEU][hapmap];1.00[EUR][1000 genomes]
rs17444498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17451053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17523074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17523307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007772	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33958791	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34898858	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34920087	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34946378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36020709	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67157227	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713527	0.92[ASN][1000 genomes]
rs878725	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv524483	chr22:29525126-29630337	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs713728	DRG1	cis	parietal	SCAN
rs713728	MMP11	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29483400-29550200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr22:29490400-29539800	Weak transcription	Psoas Muscle	Psoas
3	chr22:29517200-29546200	Strong transcription	Dnd41	blood
4	chr22:29522400-29541600	Weak transcription	HMEC	breast
5	chr22:29523400-29548200	Weak transcription	Stomach Mucosa	stomach
6	chr22:29525800-29544400	Weak transcription	NHLF	lung
7	chr22:29526200-29542800	Weak transcription	Fetal Heart	heart
8	chr22:29526200-29547000	Weak transcription	K562	blood
9	chr22:29527600-29548000	Strong transcription	Fetal Intestine Small	intestine
10	chr22:29528000-29539000	Strong transcription	Ovary	ovary
11	chr22:29528600-29544400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:29529400-29547000	Strong transcription	Thymus	Thymus
13	chr22:29530000-29541400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:29530800-29546800	Genic enhancers	Fetal Muscle Leg	muscle
15	chr22:29531000-29540800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr22:29531000-29541000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr22:29531200-29539000	Strong transcription	Esophagus	oesophagus
18	chr22:29531600-29542800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:29531600-29548400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29532600-29538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:29532800-29538600	Strong transcription	Left Ventricle	heart
22	chr22:29533000-29543200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:29533000-29545600	Strong transcription	Fetal Intestine Large	intestine
24	chr22:29533200-29543200	Strong transcription	Fetal Stomach	stomach
25	chr22:29533400-29538800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr22:29533400-29539400	Strong transcription	Brain Anterior Caudate	brain
27	chr22:29533600-29542400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr22:29533800-29539800	Strong transcription	Brain Germinal Matrix	brain
29	chr22:29533800-29543600	Strong transcription	Fetal Brain Female	brain
30	chr22:29534600-29540600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:29534800-29540400	Weak transcription	Gastric	stomach
32	chr22:29534800-29545600	Weak transcription	Aorta	Aorta
33	chr22:29535400-29540600	Weak transcription	NHEK	skin
34	chr22:29535600-29539400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr22:29535800-29538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr22:29535800-29538600	Strong transcription	Lung	lung
37	chr22:29535800-29538800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr22:29535800-29538800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29536000-29541000	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr22:29536200-29538600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr22:29536400-29538600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr22:29536400-29539400	Strong transcription	Fetal Thymus	thymus
43	chr22:29536400-29539600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:29536400-29539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr22:29536400-29540200	Weak transcription	Spleen	Spleen
46	chr22:29536400-29542400	Weak transcription	Brain Substantia Nigra	brain
47	chr22:29536400-29543000	Weak transcription	Brain Angular Gyrus	brain
48	chr22:29536600-29538800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr22:29536600-29543000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr22:29536600-29548200	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links