Variant report

Variant	rs713875
Chromosome Location	chr22:30592487-30592488
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30590030..30593992-chr22:30596510..30599068,3	K562	blood:
2	chr22:30589990..30596479-chr22:30639909..30648381,15	MCF-7	breast:
3	chr22:30578652..30582637-chr22:30590732..30593754,4	K562	blood:
4	chr11:9594464..9595108-chr22:30591798..30592673,2	Hela-S3	cervix:
5	chr22:30538829..30541820-chr22:30591024..30593094,2	K562	blood:
6	chr22:30584790..30588358-chr22:30588911..30595947,7	MCF-7	breast:
7	chr22:30592375..30593020-chr7:75676928..75677729,2	Hela-S3	cervix:
8	chr22:30592298..30595321-chr22:30600135..30602217,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146701	Chromatin interaction
ENSG00000128342	Chromatin interaction
ENSG00000127952	Chromatin interaction
ENSG00000268812	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1003342	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193477	0.80[EUR][1000 genomes]
rs2412970	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2412971	0.85[EUR][1000 genomes]
rs2412975	0.85[EUR][1000 genomes]
rs4823073	0.85[EUR][1000 genomes]
rs4823074	0.85[EUR][1000 genomes]
rs4823075	0.84[EUR][1000 genomes]
rs4823077	0.88[EUR][1000 genomes]
rs5763767	0.85[EUR][1000 genomes]
rs5997579	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6006356	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs714027	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757024	0.92[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	21102463	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs713875	ASCC2	cis	cerebellum	SCAN
rs713875	TTC28	cis	cerebellum	SCAN
rs713875	NEFH	cis	cerebellum	SCAN
rs713875	CRYBB3	cis	parietal	SCAN
rs713875	MTMR3	cis	multi-tissue	Pritchard
rs713875	MTMR3	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30588200-30593600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr22:30590400-30593400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr22:30590800-30592600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr22:30590800-30593400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr22:30590800-30593600	Enhancers	Fetal Thymus	thymus
6	chr22:30591200-30593400	Enhancers	Stomach Mucosa	stomach
7	chr22:30591200-30593600	Enhancers	Fetal Stomach	stomach
8	chr22:30591200-30593800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:30591200-30593800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr22:30591200-30595200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr22:30591400-30592600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr22:30591400-30592600	Enhancers	Brain Anterior Caudate	brain
13	chr22:30591400-30592600	Enhancers	Esophagus	oesophagus
14	chr22:30591400-30592600	Enhancers	Pancreas	Pancrea
15	chr22:30591400-30592600	Flanking Active TSS	HepG2	liver
16	chr22:30591400-30592800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:30591400-30592800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr22:30591400-30592800	Enhancers	Colon Smooth Muscle	Colon
19	chr22:30591400-30592800	Enhancers	Gastric	stomach
20	chr22:30591400-30593200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:30591400-30593200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr22:30591400-30593200	Enhancers	Right Atrium	heart
23	chr22:30591400-30593200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr22:30591400-30593200	Enhancers	Spleen	Spleen
25	chr22:30591400-30593400	Enhancers	Fetal Intestine Small	intestine
26	chr22:30591400-30593400	Enhancers	Placenta	Placenta
27	chr22:30591400-30593600	Enhancers	Fetal Intestine Large	intestine
28	chr22:30591400-30594000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr22:30591400-30595000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr22:30591600-30592600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:30591600-30592800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr22:30591600-30592800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr22:30591600-30592800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr22:30591600-30593000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:30591600-30593200	Enhancers	Primary B cells from peripheral blood	blood
36	chr22:30591600-30593200	Flanking Active TSS	HUVEC	blood vessel
37	chr22:30591600-30593400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr22:30591600-30593400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr22:30591600-30593600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr22:30591600-30593600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:30591600-30593600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr22:30591800-30592600	Flanking Active TSS	Fetal Kidney	kidney
43	chr22:30591800-30592600	Flanking Active TSS	Fetal Lung	lung
44	chr22:30591800-30592600	Flanking Active TSS	HSMM	muscle
45	chr22:30591800-30592600	Enhancers	NH-A	brain
46	chr22:30591800-30592800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:30591800-30592800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:30591800-30593000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:30591800-30593000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr22:30591800-30593200	Enhancers	Right Ventricle	heart

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