Variant report

Variant	rs6695989
Chromosome Location	chr1:78006340-78006341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM73A-2	chr1:78006181-78006374	NONHSAT004030

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013399	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782654	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10873951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11162362	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162363	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162364	0.95[AFR][1000 genomes];0.97[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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095064	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12142671	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.93[ASN][1000 genomes]
rs12724560	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565850	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565851	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]
rs1565852	0.89[ASN][1000 genomes]
rs1962523	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs1976334	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2029768	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133202	0.87[ASN][1000 genomes]
rs2172727	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647486	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647487	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs278854	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs278862	0.81[ASN][1000 genomes]
rs2803136	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs2803168	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34773766	0.92[ASN][1000 genomes]
rs3509	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs371076	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3738079	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767030	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs3767032	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767033	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4245658	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4589153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949657	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949658	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]
rs4949659	0.93[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949807	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949808	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4949811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949813	0.94[ASN][1000 genomes]
rs4949814	0.81[YRI][hapmap]
rs4949816	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs6603952	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6603953	0.94[ASN][1000 genomes]
rs6603955	0.93[ASN][1000 genomes]
rs6667519	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6667803	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675743	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6692369	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728741	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7513619	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7519476	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524147	0.97[ASN][1000 genomes]
rs7524866	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7531286	0.89[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];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551211	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551729	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552291	0.83[MKK][hapmap]
rs872342	0.83[CHD][hapmap]
rs962388	0.94[ASN][1000 genomes]
rs9787153	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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
rs6695989	PIGK	cis	parietal	SCAN
rs6695989	AK5	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
8	chr1:78001400-78006600	Enhancers	NHEK	skin
9	chr1:78001600-78006600	Enhancers	HMEC	breast
10	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:78004200-78007800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:78004400-78006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:78004400-78007600	Enhancers	GM12878-XiMat	blood
14	chr1:78004600-78006400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:78004600-78006600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:78004600-78006600	Flanking Active TSS	Osteobl	bone
17	chr1:78004600-78008200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:78004800-78006400	Flanking Active TSS	Hela-S3	cervix
19	chr1:78004800-78006600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:78004800-78007400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:78004800-78010800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:78005000-78006400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:78005000-78006600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:78005000-78007400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:78005200-78007400	Enhancers	Placenta	Placenta
26	chr1:78005200-78008000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:78005400-78006400	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:78005400-78006600	Enhancers	NHLF	lung
29	chr1:78005400-78006800	Enhancers	NHDF-Ad	bronchial
30	chr1:78005400-78007000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:78005400-78007000	Weak transcription	Fetal Kidney	kidney
32	chr1:78005400-78007600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:78005600-78007400	Enhancers	Primary B cells from peripheral blood	blood
34	chr1:78005600-78010200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78005600-78010400	Weak transcription	Fetal Heart	heart
36	chr1:78005600-78014000	Weak transcription	Right Ventricle	heart
37	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:78005800-78006400	Strong transcription	Brain Anterior Caudate	brain
39	chr1:78005800-78006600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:78005800-78010800	Weak transcription	Brain Angular Gyrus	brain
41	chr1:78005800-78011000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:78005800-78014000	Weak transcription	Right Atrium	heart
43	chr1:78005800-78026200	Weak transcription	Left Ventricle	heart
44	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
45	chr1:78006000-78006400	Genic enhancers	Brain Hippocampus Middle	brain
46	chr1:78006000-78006400	Genic enhancers	HSMM	muscle
47	chr1:78006000-78006600	Enhancers	NH-A	brain
48	chr1:78006000-78007800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:78006000-78010000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:78006000-78011400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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