Variant report

Variant	rs12642449
Chromosome Location	chr4:95508755-95508756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95508126..95511590-chr4:95512972..95515288,3	K562	blood:
2	chr4:95506991..95508792-chr4:95517105..95519106,2	K562	blood:
3	chr4:95508126..95510888-chr4:95512972..95515677,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10019142	0.84[AMR][1000 genomes]
rs10019505	0.83[ASN][1000 genomes]
rs10033326	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10034824	0.87[CHB][hapmap]
rs11724023	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs11732687	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs12500426	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12639623	0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap]
rs12639887	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639980	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645971	0.82[CHB][hapmap]
rs12648941	0.82[ASN][1000 genomes]
rs12649976	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs13110115	0.82[CHB][hapmap]
rs13122786	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135257	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13143502	0.85[CHB][hapmap]
rs17394213	0.81[ASN][1000 genomes]
rs2047025	0.89[CEU][hapmap]
rs2172448	0.83[ASN][1000 genomes]
rs2452010	0.82[CHB][hapmap]
rs2452574	0.82[CHB][hapmap]
rs2452575	0.82[CHB][hapmap]
rs2452580	0.86[CHB][hapmap]
rs2452601	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2510768	0.81[ASN][1000 genomes]
rs2510769	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2510772	0.82[CHB][hapmap]
rs2510781	0.82[CHB][hapmap]
rs28740868	0.82[EUR][1000 genomes]
rs3805263	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805264	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805266	0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs3843444	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs4634230	0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs4699505	0.81[CHB][hapmap]
rs5013417	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60063444	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532491	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6854173	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs7662466	0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7697149	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs902981	0.86[CHB][hapmap]
rs973995	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12642449	ATOH1	cis	cerebellum	SCAN
rs12642449	PDLIM5	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95489200-95509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
6	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
7	chr4:95497200-95511000	Weak transcription	Ovary	ovary
8	chr4:95497200-95512600	Weak transcription	Aorta	Aorta
9	chr4:95497200-95512600	Weak transcription	Pancreas	Pancrea
10	chr4:95497200-95513800	Weak transcription	Right Ventricle	heart
11	chr4:95497200-95516200	Weak transcription	Right Atrium	heart
12	chr4:95497200-95520000	Weak transcription	Spleen	Spleen
13	chr4:95497200-95524600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:95497200-95524600	Weak transcription	Gastric	stomach
15	chr4:95497200-95524600	Weak transcription	Lung	lung
16	chr4:95497200-95526000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
19	chr4:95497400-95510200	Weak transcription	Fetal Kidney	kidney
20	chr4:95497400-95513600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:95497400-95515000	Weak transcription	Colonic Mucosa	Colon
22	chr4:95497400-95524200	Weak transcription	NHLF	lung
23	chr4:95497400-95526200	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:95497400-95542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:95497600-95509200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:95497600-95510400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:95497600-95513600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:95497600-95539200	Weak transcription	HepG2	liver
29	chr4:95497800-95508800	Weak transcription	Fetal Thymus	thymus
30	chr4:95498400-95526200	Weak transcription	Brain Anterior Caudate	brain
31	chr4:95498600-95513400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:95498800-95511800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:95499000-95516400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:95499800-95510200	Weak transcription	NHDF-Ad	bronchial
35	chr4:95499800-95515400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:95501200-95510000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:95502800-95512600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:95503200-95516000	Weak transcription	Stomach Mucosa	stomach
39	chr4:95504000-95509800	Weak transcription	Fetal Heart	heart
40	chr4:95504200-95510400	Strong transcription	HUVEC	blood vessel
41	chr4:95504600-95517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:95505000-95510600	Strong transcription	A549	lung
43	chr4:95505000-95511600	Strong transcription	NH-A	brain
44	chr4:95505000-95515000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:95505200-95516800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:95505400-95509800	Strong transcription	Osteobl	bone
47	chr4:95505400-95510200	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:95505400-95515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr4:95505600-95510200	Strong transcription	HSMM	muscle
50	chr4:95505600-95513000	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links