Variant report

Variant	rs4949813
Chromosome Location	chr1:78027725-78027726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1013399	0.89[ASN][1000 genomes]
rs10782654	0.94[ASN][1000 genomes]
rs10873949	0.94[ASN][1000 genomes]
rs10873950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873951	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11162362	0.94[ASN][1000 genomes]
rs11162364	0.95[ASN][1000 genomes]
rs11162365	0.99[ASN][1000 genomes]
rs11162369	0.92[ASN][1000 genomes]
rs11162372	0.89[ASN][1000 genomes]
rs12071212	0.91[ASN][1000 genomes]
rs12074409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12095064	0.91[ASN][1000 genomes]
rs12128041	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs12142671	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs12717767	0.99[ASN][1000 genomes]
rs12724560	0.94[ASN][1000 genomes]
rs1565850	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs1565851	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565852	0.95[ASN][1000 genomes]
rs1962523	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976334	0.88[ASN][1000 genomes]
rs2029768	0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2133202	0.82[ASN][1000 genomes]
rs2172727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274123	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs2647486	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2647487	0.90[ASN][1000 genomes]
rs278845	0.84[ASN][1000 genomes]
rs278847	0.85[ASN][1000 genomes]
rs278852	0.83[ASN][1000 genomes]
rs278854	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs278862	0.87[ASN][1000 genomes]
rs2803136	0.89[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2803168	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs34773766	0.88[ASN][1000 genomes]
rs3509	0.89[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs371076	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3738079	0.91[ASN][1000 genomes]
rs3767030	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs3767032	0.90[ASN][1000 genomes]
rs3767033	0.89[ASN][1000 genomes]
rs4245658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4589153	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4600093	1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4949657	0.87[ASN][1000 genomes]
rs4949658	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4949659	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4949807	0.92[ASN][1000 genomes]
rs4949808	0.94[ASN][1000 genomes]
rs4949809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949816	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6603953	0.88[ASN][1000 genomes]
rs6603955	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6667519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667803	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6675743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692369	0.93[ASN][1000 genomes]
rs6695989	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6696083	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs728741	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513619	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7519476	0.94[ASN][1000 genomes]
rs7524147	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524866	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531286	1.00[ASW][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7545544	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7551211	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7551729	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs872342	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs962388	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787153	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4949813	AK5	cis	cerebellum	SCAN
rs4949813	AK5	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
5	chr1:78006000-78031000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
7	chr1:78007800-78028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:78012000-78031000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:78012600-78031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:78014400-78030600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:78014400-78031800	Weak transcription	Right Ventricle	heart
12	chr1:78014600-78027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:78016000-78030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:78017800-78031000	Weak transcription	HepG2	liver
15	chr1:78019600-78031200	Weak transcription	Fetal Heart	heart
16	chr1:78019800-78028400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:78019800-78029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:78019800-78031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:78019800-78031200	Weak transcription	K562	blood
20	chr1:78020000-78028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:78021600-78030600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:78021800-78028400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:78022200-78030200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:78022200-78030800	Weak transcription	Hela-S3	cervix
25	chr1:78022400-78030600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:78022400-78032400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:78022600-78034000	Strong transcription	Primary T cells from cord blood	blood
28	chr1:78022800-78030200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:78022800-78031000	Weak transcription	Spleen	Spleen
30	chr1:78023000-78028000	Weak transcription	HMEC	breast
31	chr1:78023000-78028200	Weak transcription	Placenta	Placenta
32	chr1:78023000-78028800	Weak transcription	Fetal Intestine Large	intestine
33	chr1:78023000-78031000	Weak transcription	Fetal Brain Female	brain
34	chr1:78023200-78028200	Weak transcription	Esophagus	oesophagus
35	chr1:78023200-78030800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:78023200-78031000	Weak transcription	Ovary	ovary
37	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:78023400-78028400	Weak transcription	HUVEC	blood vessel
39	chr1:78023400-78030600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:78023400-78031000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:78023400-78046200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:78023600-78028400	Weak transcription	Fetal Kidney	kidney
43	chr1:78023600-78029800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:78023600-78035800	Strong transcription	HSMM	muscle
45	chr1:78023800-78029000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:78023800-78030800	Weak transcription	Brain Germinal Matrix	brain
47	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:78024000-78028200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:78024000-78028200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:78024200-78028600	Strong transcription	Muscle Satellite Cultured Cells	--

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