Variant report

Variant	rs6574404
Chromosome Location	chr14:78282943-78282944
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1006038	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1006039	0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1006040	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1008988	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10139492	0.85[CHB][hapmap]
rs10142722	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs10143294	0.86[CHB][hapmap]
rs10144448	0.86[CHB][hapmap]
rs10148373	1.00[ASN][1000 genomes]
rs10149619	0.82[ASN][1000 genomes]
rs1048147	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs10483885	0.86[CHB][hapmap]
rs11159288	0.82[ASN][1000 genomes]
rs114763	0.86[CHB][hapmap]
rs11628888	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12435761	0.87[ASN][1000 genomes]
rs12883228	0.99[ASN][1000 genomes]
rs12885306	0.86[CHB][hapmap]
rs12890728	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[ASN][1000 genomes]
rs1469018	0.97[ASN][1000 genomes]
rs1477259	0.87[ASN][1000 genomes]
rs1477260	0.87[ASN][1000 genomes]
rs1477261	0.84[ASN][1000 genomes]
rs1477262	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1477264	0.86[CHB][hapmap]
rs1549119	0.84[ASN][1000 genomes]
rs17106157	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs176941	0.86[CHB][hapmap]
rs176943	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs176946	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs176951	0.95[CHB][hapmap]
rs176955	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs176956	0.86[CHB][hapmap]
rs176959	0.86[CHB][hapmap]
rs176963	0.86[CHB][hapmap]
rs176964	0.95[CHB][hapmap]
rs176965	0.86[CHB][hapmap]
rs176980	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs1978416	0.85[ASN][1000 genomes]
rs1984925	0.84[ASN][1000 genomes]
rs2032781	0.82[ASN][1000 genomes]
rs2112136	0.87[ASN][1000 genomes]
rs2267756	0.86[CHB][hapmap]
rs2267759	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2267760	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2267761	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2267762	0.86[CHB][hapmap]
rs2267763	0.86[CHB][hapmap]
rs2267764	0.86[CHB][hapmap]
rs2267767	0.81[ASN][1000 genomes]
rs2267768	0.82[ASN][1000 genomes]
rs2277917	0.86[CHB][hapmap]
rs2284234	0.86[CHB][hapmap]
rs2284235	0.86[CHB][hapmap]
rs2299930	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs2364840	1.00[ASN][1000 genomes]
rs2364841	0.80[ASN][1000 genomes]
rs3759728	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3783980	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4632066	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4899670	0.86[CHB][hapmap]
rs4899673	0.86[CHB][hapmap]
rs4903643	0.87[ASN][1000 genomes]
rs6574391	0.81[ASN][1000 genomes]
rs6574399	0.86[CHB][hapmap]
rs6574402	0.87[ASN][1000 genomes]
rs7142390	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7143926	0.86[CHB][hapmap]
rs7148078	0.82[CHB][hapmap]
rs7151685	0.86[CHB][hapmap]
rs717683	0.85[ASN][1000 genomes]
rs759713	0.86[CHB][hapmap]
rs759808	0.87[ASN][1000 genomes]
rs8003691	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs8003979	0.82[ASN][1000 genomes]
rs8011337	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs8014635	0.85[ASN][1000 genomes]
rs8015645	0.86[CHB][hapmap]
rs8016175	0.82[ASN][1000 genomes]
rs8016447	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs8018741	0.87[ASN][1000 genomes]
rs8018971	0.87[ASN][1000 genomes]
rs9323649	0.85[CHB][hapmap]
rs9323650	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs9323651	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6574404	POMT2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78267200-78284800	Weak transcription	Brain Angular Gyrus	brain
2	chr14:78267200-78285200	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:78267200-78285200	Weak transcription	Fetal Stomach	stomach
4	chr14:78267200-78285400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr14:78267200-78285400	Weak transcription	Lung	lung
6	chr14:78267200-78288200	Weak transcription	Spleen	Spleen
7	chr14:78267200-78288800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:78267200-78304200	Weak transcription	HSMMtube	muscle
9	chr14:78267200-78310800	Weak transcription	Esophagus	oesophagus
10	chr14:78267400-78285000	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:78267400-78285000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:78267400-78285200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:78267400-78285400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr14:78267600-78285000	Weak transcription	Primary T cells from cord blood	blood
15	chr14:78267600-78285400	Weak transcription	Brain Substantia Nigra	brain
16	chr14:78267800-78285400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:78270800-78288400	Weak transcription	Fetal Intestine Small	intestine
18	chr14:78270800-78288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr14:78272400-78285200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:78273000-78285400	Weak transcription	Psoas Muscle	Psoas
21	chr14:78273400-78285200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr14:78273400-78285400	Weak transcription	Left Ventricle	heart
23	chr14:78274800-78316600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:78279400-78285400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:78280000-78287600	Weak transcription	K562	blood
26	chr14:78280600-78285600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr14:78280800-78285400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:78281200-78285400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr14:78281600-78285200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr14:78282000-78285200	Weak transcription	Aorta	Aorta
31	chr14:78282000-78285200	Weak transcription	Dnd41	blood
32	chr14:78282400-78285400	Weak transcription	Right Ventricle	heart
33	chr14:78282800-78284600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:78282800-78284800	Weak transcription	Adipose Nuclei	Adipose
35	chr14:78282800-78285400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:78282800-78285400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:78282800-78285400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:78282800-78288600	Weak transcription	Pancreas	Pancrea

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