Variant report

Variant	rs1975937
Chromosome Location	chr19:38091932-38091933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF793-2	chr19:38091911-38092006	NONHSAT066146

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10402671	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10404031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10406379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10408619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409605	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10410588	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10412510	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412786	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10417576	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420268	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420552	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10425795	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083432	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs11673023	0.81[EUR][1000 genomes]
rs12459015	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12974225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12979640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531549	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564206	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1564208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16958861	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16958863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1974714	0.80[ASN][1000 genomes]
rs1975939	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075284	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279148	0.96[CHB][hapmap];0.81[YRI][hapmap]
rs2279149	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs2287229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2385119	0.82[ASN][1000 genomes]
rs241932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28512414	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909085	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2909088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2909093	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909100	0.84[EUR][1000 genomes]
rs2909102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2927739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2927740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2927742	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927746	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2927747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972430	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972434	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972445	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972446	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2972452	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2972458	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095726	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101746	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3101747	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112433	0.87[ASN][1000 genomes]
rs3112434	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35863684	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803215	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803231	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803233	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803263	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803276	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803287	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56151076	0.90[ASN][1000 genomes]
rs56317671	0.81[EUR][1000 genomes]
rs62108337	0.84[EUR][1000 genomes]
rs6508736	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8100646	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103647	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110865	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs856300	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs856304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9304568	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs958305	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs968073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9749368	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9797618	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9941475	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1975937	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38086400-38093400	Weak transcription	Gastric	stomach
2	chr19:38086400-38095600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr19:38086400-38095600	Weak transcription	Stomach Mucosa	stomach
4	chr19:38086600-38092000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:38086600-38092200	Weak transcription	Small Intestine	intestine
6	chr19:38086600-38092800	Weak transcription	Fetal Muscle Leg	muscle
7	chr19:38086600-38098200	Weak transcription	Colonic Mucosa	Colon
8	chr19:38086600-38098800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:38086600-38099400	Weak transcription	Fetal Stomach	stomach
10	chr19:38086600-38103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:38086800-38092000	Weak transcription	Fetal Lung	lung
12	chr19:38086800-38094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:38086800-38095600	Weak transcription	Fetal Kidney	kidney
14	chr19:38087200-38093200	Weak transcription	Fetal Intestine Small	intestine
15	chr19:38087200-38099400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:38087200-38100200	Weak transcription	Right Ventricle	heart
17	chr19:38087200-38103000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:38087400-38092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:38087800-38094400	Weak transcription	Fetal Brain Male	brain
20	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
21	chr19:38088800-38092200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr19:38088800-38093800	ZNF genes & repeats	Ovary	ovary
23	chr19:38088800-38094000	Strong transcription	Primary T cells from cord blood	blood
24	chr19:38088800-38094000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:38088800-38094600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:38089000-38093400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:38089000-38093800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:38089000-38094000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:38089000-38094400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:38089200-38093600	Strong transcription	Brain Substantia Nigra	brain
31	chr19:38089200-38093800	Strong transcription	Brain Angular Gyrus	brain
32	chr19:38089200-38094000	Strong transcription	Left Ventricle	heart
33	chr19:38089200-38107200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr19:38089400-38092600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:38089400-38092800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:38089400-38093400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:38089400-38093600	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:38089400-38093800	Strong transcription	Brain Cingulate Gyrus	brain
39	chr19:38089400-38094200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38089400-38094600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38089400-38095200	Strong transcription	Brain Anterior Caudate	brain
42	chr19:38089600-38092600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:38089600-38094600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr19:38089600-38095200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:38089800-38092000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:38089800-38093600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:38090400-38092400	Strong transcription	Dnd41	blood
48	chr19:38090400-38092600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
49	chr19:38090400-38093800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:38090400-38094200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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