Variant report

Variant	rs8102020
Chromosome Location	chr19:36685690-36685691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COX7A1-4	chr19:36685527-36686058	NONHSAT065968

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10409091	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10411031	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10416179	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10416237	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10417892	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418510	0.91[CHB][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs12973781	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070132	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310856	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432039	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2432042	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432043	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2432045	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2432049	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432051	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2432052	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432054	0.84[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2438514	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2438517	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28408024	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918375	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2918378	0.88[EUR][1000 genomes]
rs2918379	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2918380	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945945	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2945950	0.95[CHB][hapmap]
rs2945961	0.95[CHB][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2945972	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2945993	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2967484	0.90[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2967506	0.95[CHB][hapmap];0.81[MEX][hapmap]
rs2967517	0.86[CHB][hapmap]
rs2972321	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972537	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972542	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4239585	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806283	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6510527	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251727	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv579425	chr19:36643695-36685753	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8102020	ZNF222	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36661800-36686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:36669600-36704800	Weak transcription	Psoas Muscle	Psoas
3	chr19:36673800-36704800	Weak transcription	Fetal Kidney	kidney
4	chr19:36674000-36704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:36674200-36687200	Weak transcription	GM12878-XiMat	blood
6	chr19:36674400-36690000	Weak transcription	NHDF-Ad	bronchial
7	chr19:36674400-36704600	Weak transcription	Fetal Brain Male	brain
8	chr19:36674600-36687200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:36674600-36687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:36674600-36687400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:36674600-36687800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:36674600-36704600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:36674600-36704600	Weak transcription	HMEC	breast
14	chr19:36674600-36704600	Weak transcription	NH-A	brain
15	chr19:36674600-36704600	Weak transcription	NHEK	skin
16	chr19:36674600-36704800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr19:36674800-36694400	Weak transcription	Fetal Heart	heart
18	chr19:36682600-36686000	Strong transcription	Lung	lung
19	chr19:36682600-36686200	Strong transcription	Liver	Liver
20	chr19:36682600-36686200	Strong transcription	Brain Angular Gyrus	brain
21	chr19:36682600-36687200	Weak transcription	Hela-S3	cervix
22	chr19:36682600-36705000	Weak transcription	Small Intestine	intestine
23	chr19:36682800-36686000	Strong transcription	Fetal Intestine Small	intestine
24	chr19:36682800-36687800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:36683200-36686200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:36683200-36686200	Strong transcription	Fetal Stomach	stomach
27	chr19:36683400-36686000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:36683600-36686000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:36683600-36686200	Strong transcription	Fetal Brain Female	brain
30	chr19:36683800-36686000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr19:36684400-36686000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:36684400-36686000	Strong transcription	Ovary	ovary
33	chr19:36684600-36685800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:36684600-36685800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:36684600-36685800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr19:36684600-36686000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:36684600-36686000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36684600-36686000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:36684600-36686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:36684600-36686000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:36684600-36686000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:36684600-36686000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:36684600-36686000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36684600-36686000	Strong transcription	Aorta	Aorta
45	chr19:36684600-36686000	Strong transcription	Brain Anterior Caudate	brain
46	chr19:36684600-36686000	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:36684600-36686000	Strong transcription	Brain Substantia Nigra	brain
48	chr19:36684600-36686000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr19:36684600-36686000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:36684600-36686000	Strong transcription	Placenta	Placenta

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