Variant report

Variant	rs12639623
Chromosome Location	chr4:95525186-95525187
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95519565..95521172-chr4:95523834..95525927,2	K562	blood:
2	chr4:95519192..95521065-chr4:95523008..95525334,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10019142	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10019505	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10033326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10034824	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724023	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs11732687	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs12500426	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639887	0.89[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs12639980	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12642449	0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap]
rs12648941	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12649976	0.92[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes]
rs13122786	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs13135257	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2047025	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs2172448	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452580	0.90[CHB][hapmap]
rs2452601	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap]
rs2510769	0.86[CHB][hapmap]
rs2510772	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2510777	0.81[CHD][hapmap]
rs28740868	0.83[ASN][1000 genomes]
rs3805263	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs3805266	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3843444	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4634230	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5013417	0.88[CEU][hapmap];0.80[CHB][hapmap]
rs6532491	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6853490	0.82[EUR][1000 genomes]
rs6854173	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7662466	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs902981	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12639623	PDLIM5	cis	parietal	SCAN
rs12639623	ATOH1	cis	cerebellum	SCAN
rs12639623	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
3	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
4	chr4:95497200-95526000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
7	chr4:95497400-95526200	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:95497400-95542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:95497600-95539200	Weak transcription	HepG2	liver
10	chr4:95498400-95526200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:95507200-95548200	Weak transcription	Psoas Muscle	Psoas
12	chr4:95507200-95548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:95507800-95539200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:95508200-95526000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:95511200-95554800	Weak transcription	NHDF-Ad	bronchial
16	chr4:95512200-95526200	Weak transcription	Adipose Nuclei	Adipose
17	chr4:95512800-95526200	Weak transcription	Ovary	ovary
18	chr4:95513000-95539000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:95514200-95539200	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:95514400-95539200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:95514400-95544600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:95514600-95526200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:95514600-95530800	Weak transcription	Primary T cells from cord blood	blood
24	chr4:95514600-95539200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:95514600-95542600	Weak transcription	NHEK	skin
26	chr4:95514800-95527400	Weak transcription	Pancreas	Pancrea
27	chr4:95514800-95531200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:95514800-95532200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:95514800-95539000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:95515000-95538600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:95515000-95562000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:95516600-95525800	Weak transcription	K562	blood
33	chr4:95520200-95526000	Weak transcription	NH-A	brain
34	chr4:95520600-95532200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:95521000-95529800	Weak transcription	HMEC	breast
36	chr4:95521400-95526000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:95521400-95529000	Weak transcription	Liver	Liver
38	chr4:95521400-95531200	Weak transcription	Fetal Intestine Large	intestine
39	chr4:95521600-95526000	Weak transcription	Aorta	Aorta
40	chr4:95521600-95528400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:95521600-95528800	Weak transcription	HSMM	muscle
42	chr4:95521600-95544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:95522200-95525600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:95522200-95538200	Weak transcription	Placenta	Placenta
45	chr4:95522400-95532200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:95523000-95526000	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:95523200-95526000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:95524000-95526200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:95524000-95527200	Enhancers	HUVEC	blood vessel
50	chr4:95524200-95525200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links