Variant report

Variant	rs12649976
Chromosome Location	chr4:95544285-95544286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10031423	0.84[EUR][1000 genomes]
rs10033326	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs10034824	0.94[CHB][hapmap]
rs1043853	0.81[EUR][1000 genomes]
rs1048627	0.81[EUR][1000 genomes]
rs11097433	0.80[EUR][1000 genomes]
rs11723532	0.86[EUR][1000 genomes]
rs11724023	0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11725850	0.90[EUR][1000 genomes]
rs11732668	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11732687	0.96[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.92[EUR][1000 genomes]
rs11734014	0.87[EUR][1000 genomes]
rs12331240	0.80[EUR][1000 genomes]
rs12500426	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs12507763	0.80[EUR][1000 genomes]
rs12511111	0.81[EUR][1000 genomes]
rs12639623	0.92[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes]
rs12639887	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12639980	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12641023	0.87[EUR][1000 genomes]
rs12642449	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]
rs12650641	0.82[EUR][1000 genomes]
rs13110828	0.83[EUR][1000 genomes]
rs13122786	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13130496	0.81[EUR][1000 genomes]
rs13135257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543013	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2047025	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2280002	0.82[EUR][1000 genomes]
rs2452601	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2510769	0.87[CHB][hapmap]
rs28740868	0.84[EUR][1000 genomes]
rs2902987	0.80[EUR][1000 genomes]
rs34403066	0.87[EUR][1000 genomes]
rs34438564	0.87[EUR][1000 genomes]
rs34507709	0.81[EUR][1000 genomes]
rs35959898	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3805263	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3805264	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805266	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap]
rs3843444	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs4634230	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap]
rs4699567	0.87[EUR][1000 genomes]
rs5013417	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60063444	0.84[ASN][1000 genomes]
rs60195134	0.88[EUR][1000 genomes]
rs6532495	0.80[EUR][1000 genomes]
rs6532496	0.80[EUR][1000 genomes]
rs6532497	0.80[EUR][1000 genomes]
rs6829381	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs6853490	0.90[ASN][1000 genomes]
rs6854173	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71601224	0.88[EUR][1000 genomes]
rs7662466	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap]
rs7690296	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs7697149	0.83[EUR][1000 genomes]
rs902981	0.89[CEU][hapmap]
rs951613	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs973995	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12649976	PDLIM5	cis	parietal	SCAN
rs12649976	FAM190A	cis	cerebellum	SCAN
rs12649976	ATOH1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
4	chr4:95507200-95548200	Weak transcription	Psoas Muscle	Psoas
5	chr4:95507200-95548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:95511200-95554800	Weak transcription	NHDF-Ad	bronchial
7	chr4:95514400-95544600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:95515000-95562000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:95521600-95544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:95525000-95569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:95525000-95590000	Weak transcription	Lung	lung
13	chr4:95525400-95562200	Weak transcription	NHLF	lung
14	chr4:95526600-95544800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:95526800-95551000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
17	chr4:95528000-95555000	Weak transcription	Aorta	Aorta
18	chr4:95532400-95544600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:95533800-95594200	Weak transcription	Gastric	stomach
20	chr4:95537000-95563000	Weak transcription	K562	blood
21	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
22	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
23	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
24	chr4:95538200-95555200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
26	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:95538400-95545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:95538800-95546600	Strong transcription	Osteobl	bone
30	chr4:95538800-95547800	Weak transcription	Brain Angular Gyrus	brain
31	chr4:95539000-95553600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:95539200-95545000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:95539800-95561000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:95540000-95560600	Weak transcription	HepG2	liver
35	chr4:95540000-95566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:95540200-95545600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:95540400-95544600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:95540400-95558600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:95540400-95561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:95540400-95570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:95540600-95555000	Weak transcription	Ovary	ovary
44	chr4:95541000-95572600	Weak transcription	Small Intestine	intestine
45	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
46	chr4:95541400-95544800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:95541400-95545400	Weak transcription	Fetal Intestine Large	intestine
48	chr4:95541400-95545600	Weak transcription	HSMM	muscle
49	chr4:95541400-95550800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:95541400-95554800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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