Variant report

Variant	rs28590063
Chromosome Location	chr19:20012070-20012071
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	chr19:19650831..19653075-chr19:20010995..20012617,3	K562	blood:
5	chr19:20011703..20012262-chr20:3748393..3749228,2	NB4	blood:
6	chr19:19976218..19978192-chr19:20011161..20013662,4	K562	blood:

Variant related genes	Relation type
ENSG00000160161	Chromatin interaction
ENSG00000267565	Chromatin interaction
ENSG00000256771	Chromatin interaction
ENSG00000101220	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1019279	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407726	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10408752	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10412710	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10414919	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10415179	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10421280	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10426937	0.89[EUR][1000 genomes]
rs1048421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151060	0.82[CEU][hapmap]
rs13344370	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469700	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1469701	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17617402	0.84[ASW][hapmap]
rs2060239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2160156	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2335365	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2335366	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2335368	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2335887	0.84[ASW][hapmap]
rs386976	0.84[ASW][hapmap]
rs3943792	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808221	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4809006	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809015	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs4809016	0.84[ASN][1000 genomes]
rs55816500	0.83[EUR][1000 genomes]
rs60765256	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511059	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66970424	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252079	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253407	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7254355	0.89[EUR][1000 genomes]
rs7256224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258260	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73532705	0.83[EUR][1000 genomes]
rs8105329	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8105482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108528	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109743	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28590063	ZNF506	cis	cerebellum	SCAN
rs28590063	ATP13A1	cis	parietal	SCAN
rs28590063	HOMER3	cis	cerebellum	SCAN
rs28590063	ZNF93	cis	Thyroid	GTEx
rs28590063	ZNF253	cis	Nerve Tibial	GTEx
rs28590063	SUGP2	cis	parietal	SCAN
rs28590063	ZNF93	cis	cerebellum	SCAN
rs28590063	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs28590063	C19orf44	cis	cerebellum	SCAN
rs28590063	ZNF682	cis	Muscle Skeletal	GTEx
rs28590063	ZNF493	cis	parietal	SCAN
rs28590063	GTPBP3	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr19:20010800-20012600	Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:20010800-20012800	ZNF genes & repeats	Liver	Liver
4	chr19:20010800-20013200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:20010800-20013400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:20011000-20012400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:20011000-20012400	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr19:20011000-20012400	Active TSS	Brain Anterior Caudate	brain
9	chr19:20011000-20012400	Active TSS	Brain Substantia Nigra	brain
10	chr19:20011000-20012600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:20011000-20012600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr19:20011000-20012600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr19:20011000-20012600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr19:20011000-20012600	Active TSS	Fetal Muscle Trunk	muscle
15	chr19:20011000-20012600	Active TSS	Placenta	Placenta
16	chr19:20011000-20012600	Active TSS	Left Ventricle	heart
17	chr19:20011000-20012600	Active TSS	Lung	lung
18	chr19:20011000-20012600	Active TSS	Pancreas	Pancrea
19	chr19:20011000-20012600	Active TSS	Thymus	Thymus
20	chr19:20011000-20012600	ZNF genes & repeats	HepG2	liver
21	chr19:20011000-20012800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:20011000-20012800	Active TSS	Brain Hippocampus Middle	brain
23	chr19:20011000-20012800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:20011000-20012800	Active TSS	Colon Smooth Muscle	Colon
25	chr19:20011000-20012800	Active TSS	Fetal Stomach	stomach
26	chr19:20011000-20012800	Active TSS	Gastric	stomach
27	chr19:20011000-20012800	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr19:20011000-20012800	Active TSS	Stomach Mucosa	stomach
29	chr19:20011000-20013000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr19:20011000-20013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:20011000-20013000	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr19:20011000-20013000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:20011000-20013000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:20011000-20013000	Active TSS	Aorta	Aorta
35	chr19:20011000-20013000	Active TSS	Brain Angular Gyrus	brain
36	chr19:20011000-20013000	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:20011000-20013000	Active TSS	Duodenum Mucosa	Duodenum
38	chr19:20011000-20013000	Active TSS	Fetal Intestine Large	intestine
39	chr19:20011000-20013000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr19:20011000-20013000	Active TSS	Ovary	ovary
41	chr19:20011000-20013000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr19:20011000-20013000	Active TSS	Psoas Muscle	Psoas
43	chr19:20011000-20013000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:20011000-20013000	Active TSS	Right Ventricle	heart
45	chr19:20011000-20013000	Active TSS	GM12878-XiMat	blood
46	chr19:20011000-20013000	ZNF genes & repeats	HMEC	breast
47	chr19:20011000-20013000	Active TSS	HSMM	muscle
48	chr19:20011000-20013200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:20011000-20013200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:20011000-20013200	Active TSS	Muscle Satellite Cultured Cells	--

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