Variant report

Variant	rs4949658
Chromosome Location	chr1:78013771-78013772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78012030..78014042-chr1:78469948..78471688,2	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1013399	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873949	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873950	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10873951	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11162362	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162363	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162364	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162365	0.93[ASN][1000 genomes]
rs11162369	0.86[ASN][1000 genomes]
rs11162372	0.84[ASN][1000 genomes]
rs12071212	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074409	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095064	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128041	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs12142671	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.93[ASN][1000 genomes]
rs12724560	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565850	1.00[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565851	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565852	0.89[ASN][1000 genomes]
rs1962523	0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs1976334	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2029768	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133202	0.87[ASN][1000 genomes]
rs2172727	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274123	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs2647486	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647487	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs278854	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs278862	0.81[ASN][1000 genomes]
rs2803136	0.89[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs2803168	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34773766	0.92[ASN][1000 genomes]
rs3509	0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs371076	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3738079	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767030	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs3767032	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767033	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4245658	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4589153	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600093	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949657	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949659	0.92[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949807	0.98[ASN][1000 genomes]
rs4949808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949809	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4949811	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949813	0.94[ASN][1000 genomes]
rs4949814	0.81[YRI][hapmap]
rs4949816	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs6603952	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6603953	0.94[ASN][1000 genomes]
rs6603955	0.93[ASN][1000 genomes]
rs6667519	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6667803	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675743	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6692369	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696083	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728741	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7513619	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7519476	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524147	0.97[ASN][1000 genomes]
rs7524866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7531286	0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545544	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551211	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551729	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552291	0.88[MKK][hapmap]
rs872342	0.85[CHD][hapmap]
rs962388	0.94[ASN][1000 genomes]
rs9787153	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4949658	PIGK	cis	parietal	SCAN
rs4949658	AK5	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:78005600-78014000	Weak transcription	Right Ventricle	heart
5	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:78005800-78014000	Weak transcription	Right Atrium	heart
7	chr1:78005800-78026200	Weak transcription	Left Ventricle	heart
8	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
9	chr1:78006000-78014000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:78006000-78022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:78006000-78026200	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:78006000-78031000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:78006200-78024400	Weak transcription	HSMMtube	muscle
14	chr1:78006200-78027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
16	chr1:78007800-78028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:78009000-78014200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:78009000-78023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:78010000-78027400	Weak transcription	A549	lung
20	chr1:78010600-78013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:78010800-78017400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:78011000-78013800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:78011000-78014000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:78011600-78014000	Weak transcription	Brain Anterior Caudate	brain
25	chr1:78011800-78021000	Weak transcription	HSMM	muscle
26	chr1:78012000-78019800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:78012000-78031000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:78012200-78013800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:78012200-78017000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:78012200-78021000	Weak transcription	NHLF	lung
31	chr1:78012200-78023000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:78012200-78023800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:78012400-78014000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:78012600-78017200	Weak transcription	Primary T cells from cord blood	blood
35	chr1:78012600-78022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:78012600-78023000	Weak transcription	Osteobl	bone
37	chr1:78012600-78031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:78012800-78014000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:78012800-78014000	Weak transcription	NHDF-Ad	bronchial
40	chr1:78012800-78023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:78013600-78014400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:78013600-78014400	Enhancers	Fetal Heart	heart

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