Variant report

Variant	rs1074990
Chromosome Location	chr19:20829954-20829955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10405703	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10406397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410025	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10412797	0.81[ASN][1000 genomes]
rs10417842	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419521	0.85[ASN][1000 genomes]
rs10420114	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10421251	0.88[ASN][1000 genomes]
rs10423967	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10425311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10425331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854032	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11085368	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11085370	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11667375	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12975304	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2288534	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274801	0.86[AMR][1000 genomes]
rs274802	0.86[AMR][1000 genomes]
rs274803	0.86[AMR][1000 genomes]
rs274804	0.86[AMR][1000 genomes]
rs274805	0.86[AMR][1000 genomes]
rs274806	0.84[AMR][1000 genomes]
rs274807	0.89[AMR][1000 genomes]
rs274809	0.89[AMR][1000 genomes]
rs274810	0.81[AMR][1000 genomes]
rs274814	0.86[AFR][1000 genomes]
rs274815	0.88[AMR][1000 genomes]
rs35237192	0.81[ASN][1000 genomes]
rs4644961	0.87[AMR][1000 genomes]
rs4808254	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4808256	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4809081	0.88[ASN][1000 genomes]
rs4809083	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4809084	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7247393	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7252292	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7254057	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7254509	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256231	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7258892	0.99[ASN][1000 genomes]
rs7259846	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100262	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8100360	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8100509	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8100596	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8112343	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9304973	0.82[ASN][1000 genomes]
rs959419	0.86[AMR][1000 genomes]
rs9917099	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9917105	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
2	esv2758489	chr19:20574295-20845947	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758749	chr19:20574295-20845947	ZNF genes & repeats Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530804	chr19:20574295-21001349	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
5	nsv978786	chr19:20818886-20884983	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911407	chr19:20818886-20885811	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911408	chr19:20818886-20885811	Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1065039	chr19:20818886-20977326	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv2751781	chr19:20818886-20985425	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv578921	chr19:20818886-20985425	ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv458510	chr19:20818886-20987550	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv578910	chr19:20818886-20987550	Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv578917	chr19:20818886-20989873	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv578918	chr19:20818886-21008212	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv3447275	chr19:20818886-21030779	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	esv2752729	chr19:20818886-21169554	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
19	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1074990	ZNF626	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20814600-20842200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:20815000-20843400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:20815200-20843200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:20816200-20831000	ZNF genes & repeats	Liver	Liver
5	chr19:20816200-20843000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr19:20816400-20842600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:20821000-20842400	Weak transcription	K562	blood
8	chr19:20822600-20840000	Weak transcription	Psoas Muscle	Psoas
9	chr19:20822600-20842200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:20822600-20842800	Weak transcription	HSMMtube	muscle
11	chr19:20823600-20843200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:20824800-20832800	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:20825400-20839400	Weak transcription	Brain Anterior Caudate	brain
14	chr19:20825600-20832400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:20825600-20840800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:20826800-20832600	Weak transcription	Stomach Mucosa	stomach
17	chr19:20827000-20831800	Weak transcription	NHDF-Ad	bronchial
18	chr19:20827000-20838400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:20827000-20840800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:20827000-20841000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:20827000-20841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:20827000-20842400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:20827000-20842800	Weak transcription	Gastric	stomach
24	chr19:20827200-20830400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:20827200-20830600	Weak transcription	Lung	lung
26	chr19:20827200-20830600	Weak transcription	NHEK	skin
27	chr19:20827200-20831800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:20827200-20832000	Weak transcription	HSMM	muscle
29	chr19:20827200-20833800	Weak transcription	Placenta	Placenta
30	chr19:20827200-20834000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:20827200-20834000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:20827200-20834200	Weak transcription	Ovary	ovary
33	chr19:20827200-20834400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:20827200-20837000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:20827200-20837600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:20827200-20839800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:20827200-20840000	Weak transcription	Brain Substantia Nigra	brain
38	chr19:20827200-20841000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:20827200-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr19:20827200-20841200	Weak transcription	Pancreas	Pancrea
41	chr19:20827200-20841200	Weak transcription	Right Ventricle	heart
42	chr19:20827200-20842600	Weak transcription	Brain Angular Gyrus	brain
43	chr19:20827400-20830400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:20827400-20830600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:20827400-20830600	Weak transcription	Brain Germinal Matrix	brain
46	chr19:20827400-20830600	Weak transcription	Fetal Thymus	thymus
47	chr19:20827400-20831800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:20827400-20832000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:20827400-20837000	Weak transcription	Left Ventricle	heart
50	chr19:20827400-20839400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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