Variant report

Variant	rs4809007
Chromosome Location	chr19:20012641-20012642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:20004584..20007360-chr19:20011373..20013192,2	K562	blood:
2	chr19:19976692..19979119-chr19:20011140..20013486,2	K562	blood:
3	chr19:20012007..20015625-chr19:20016618..20018648,3	K562	blood:
4	chr19:19976218..19978192-chr19:20011161..20013662,4	K562	blood:

Variant related genes	Relation type
ENSG00000256771	Chromatin interaction
ENSG00000267565	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1008112	0.83[EUR][1000 genomes]
rs1019280	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11085283	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666112	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668581	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670634	0.86[EUR][1000 genomes]
rs12151060	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460570	0.83[EUR][1000 genomes]
rs12608906	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12610295	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2110587	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2110589	0.82[EUR][1000 genomes]
rs2160157	0.83[EUR][1000 genomes]
rs258575	0.80[EUR][1000 genomes]
rs258579	0.82[EUR][1000 genomes]
rs4808223	0.86[EUR][1000 genomes]
rs4809005	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4809014	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58151139	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60549783	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61699225	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255064	0.83[EUR][1000 genomes]
rs73008647	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73008648	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73008668	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73008670	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109457	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111124	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
15	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
16	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers 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	43 gene(s)	inside rSNPs	diseases
17	esv3407363	chr19:20000919-20059307	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv1845482	chr19:20006144-20014389	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4809007	ZNF253	Cis_1M	lymphoblastoid	RTeQTL
rs4809007	ZNF682	cis	Muscle Skeletal	GTEx
rs4809007	ZNF253	cis	Heart Left Ventricle	GTEx
rs4809007	ZNF253	cis	Nerve Tibial	GTEx
rs4809007	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20010600-20013000	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr19:20010800-20012800	ZNF genes & repeats	Liver	Liver
3	chr19:20010800-20013200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:20010800-20013400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:20011000-20012800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:20011000-20012800	Active TSS	Brain Hippocampus Middle	brain
7	chr19:20011000-20012800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:20011000-20012800	Active TSS	Colon Smooth Muscle	Colon
9	chr19:20011000-20012800	Active TSS	Fetal Stomach	stomach
10	chr19:20011000-20012800	Active TSS	Gastric	stomach
11	chr19:20011000-20012800	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:20011000-20012800	Active TSS	Stomach Mucosa	stomach
13	chr19:20011000-20013000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:20011000-20013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:20011000-20013000	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr19:20011000-20013000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:20011000-20013000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:20011000-20013000	Active TSS	Aorta	Aorta
19	chr19:20011000-20013000	Active TSS	Brain Angular Gyrus	brain
20	chr19:20011000-20013000	Active TSS	Brain Cingulate Gyrus	brain
21	chr19:20011000-20013000	Active TSS	Duodenum Mucosa	Duodenum
22	chr19:20011000-20013000	Active TSS	Fetal Intestine Large	intestine
23	chr19:20011000-20013000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:20011000-20013000	Active TSS	Ovary	ovary
25	chr19:20011000-20013000	Active TSS	Placenta Amnion	Placenta Amnion
26	chr19:20011000-20013000	Active TSS	Psoas Muscle	Psoas
27	chr19:20011000-20013000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr19:20011000-20013000	Active TSS	Right Ventricle	heart
29	chr19:20011000-20013000	Active TSS	GM12878-XiMat	blood
30	chr19:20011000-20013000	ZNF genes & repeats	HMEC	breast
31	chr19:20011000-20013000	Active TSS	HSMM	muscle
32	chr19:20011000-20013200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:20011000-20013200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:20011000-20013200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:20011000-20013200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:20011000-20013200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:20011000-20013200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:20011000-20013200	Active TSS	Rectal Smooth Muscle	rectum
39	chr19:20011000-20013200	Active TSS	NH-A	brain
40	chr19:20011000-20013200	Active TSS	NHDF-Ad	bronchial
41	chr19:20011000-20013200	Active TSS	NHEK	skin
42	chr19:20011000-20013200	Active TSS	NHLF	lung
43	chr19:20011000-20013400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr19:20011000-20013400	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr19:20011000-20013400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:20011000-20013400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:20011000-20013400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:20011000-20013400	Active TSS	Colonic Mucosa	Colon
49	chr19:20011000-20013400	Active TSS	Fetal Kidney	kidney
50	chr19:20011000-20013400	Active TSS	Osteobl	bone

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