Variant report

Variant	rs1565851
Chromosome Location	chr1:78022217-78022218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78020809..78023858-chr1:78146827..78149846,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1013399	0.93[ASN][1000 genomes]
rs10782654	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873949	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873950	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873951	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11162362	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162364	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162365	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11162366	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11162369	0.88[ASN][1000 genomes]
rs11162372	0.85[ASN][1000 genomes]
rs12071212	0.95[ASN][1000 genomes]
rs12074409	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095064	0.95[ASN][1000 genomes]
rs12128041	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs12142671	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.95[ASN][1000 genomes]
rs12724560	0.98[ASN][1000 genomes]
rs1565850	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565852	0.91[ASN][1000 genomes]
rs1962523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976334	0.92[ASN][1000 genomes]
rs2029768	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2133202	0.85[ASN][1000 genomes]
rs2172727	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2274123	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs2296227	0.82[LWK][hapmap]
rs2647486	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2647487	0.94[ASN][1000 genomes]
rs278845	0.81[ASN][1000 genomes]
rs278847	0.81[ASN][1000 genomes]
rs278854	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs278862	0.83[ASN][1000 genomes]
rs2803136	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2803168	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34773766	0.92[ASN][1000 genomes]
rs3509	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs371076	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3738079	0.95[ASN][1000 genomes]
rs3767030	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap]
rs3767032	0.94[ASN][1000 genomes]
rs3767033	0.93[ASN][1000 genomes]
rs4245658	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4589153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4600093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949657	0.91[ASN][1000 genomes]
rs4949658	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]
rs4949659	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949661	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4949807	0.97[ASN][1000 genomes]
rs4949808	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949809	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949811	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949813	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949814	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4949816	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6603953	0.93[ASN][1000 genomes]
rs6603955	0.95[ASN][1000 genomes]
rs6667519	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6670660	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6675743	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691317	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6692369	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695989	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696083	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs6698151	0.84[AMR][1000 genomes]
rs728741	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513619	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7519476	0.98[ASN][1000 genomes]
rs7524147	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524866	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531286	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7545175	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7545544	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs7546365	0.82[ASW][hapmap];0.85[LWK][hapmap]
rs7551211	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7551729	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7552291	0.94[ASW][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs872342	0.85[CHD][hapmap]
rs962388	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787153	0.95[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
rs1565851	AK5	cis	parietal	SCAN
rs1565851	PIGK	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

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	chr1:78005800-78026200	Weak transcription	Left Ventricle	heart
5	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
6	chr1:78006000-78022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:78006000-78026200	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:78006000-78031000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:78006200-78024400	Weak transcription	HSMMtube	muscle
10	chr1:78006200-78027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
12	chr1:78007800-78028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:78009000-78023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:78010000-78027400	Weak transcription	A549	lung
15	chr1:78012000-78031000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:78012200-78023000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:78012200-78023800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:78012600-78022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:78012600-78023000	Weak transcription	Osteobl	bone
20	chr1:78012600-78031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:78012800-78023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:78014200-78024200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:78014200-78026000	Weak transcription	Brain Anterior Caudate	brain
24	chr1:78014400-78022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:78014400-78024200	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:78014400-78030600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:78014400-78031800	Weak transcription	Right Ventricle	heart
28	chr1:78014600-78022600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:78014600-78023200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:78014600-78024600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:78014600-78027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:78015800-78024400	Weak transcription	Fetal Intestine Small	intestine
33	chr1:78016000-78030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:78017400-78023400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:78017800-78031000	Weak transcription	HepG2	liver
36	chr1:78019200-78026200	Weak transcription	NH-A	brain
37	chr1:78019200-78027200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:78019600-78031200	Weak transcription	Fetal Heart	heart
39	chr1:78019800-78026000	Weak transcription	NHEK	skin
40	chr1:78019800-78028400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:78019800-78029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:78019800-78031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:78019800-78031200	Weak transcription	K562	blood
44	chr1:78020000-78022600	Weak transcription	Pancreas	Pancrea
45	chr1:78020000-78028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:78020200-78022600	Weak transcription	Primary T cells from cord blood	blood
47	chr1:78020200-78023000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:78020200-78024600	Weak transcription	Gastric	stomach
49	chr1:78020200-78025800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:78021400-78022400	Enhancers	Primary neutrophils fromperipheralblood	blood

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