Variant report

Variant	rs7258575
Chromosome Location	chr19:21344190-21344191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10406253	0.93[JPT][hapmap]
rs10408496	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs10414473	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415009	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854042	0.93[JPT][hapmap]
rs11668640	0.85[AFR][1000 genomes]
rs11671623	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980860	0.85[AFR][1000 genomes]
rs2115498	0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap]
rs2358807	0.82[AFR][1000 genomes]
rs4324267	0.82[JPT][hapmap]
rs6511202	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs6511204	0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs6511205	0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6511206	0.94[JPT][hapmap]
rs6511207	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7247730	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7250987	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7251158	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7251646	0.94[JPT][hapmap]
rs7254094	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256576	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs7257196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7259368	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8101918	1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs8108314	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8110848	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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
2	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7258575	TMEM59L	cis	parietal	SCAN
rs7258575	ZNF708	cis	cerebellum	SCAN
rs7258575	ZNF682	cis	cerebellum	SCAN
rs7258575	ZNF100	cis	cerebellum	SCAN
rs7258575	ZNF208	cis	parietal	SCAN
rs7258575	NDUFA13	cis	cerebellum	SCAN
rs7258575	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7258575	ZNF714	cis	parietal	SCAN
rs7258575	ZNF714	cis	cerebellum	SCAN
rs7258575	ZNF493	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21325400-21361800	Weak transcription	Small Intestine	intestine
2	chr19:21325600-21365800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:21326000-21352600	Weak transcription	Right Ventricle	heart
4	chr19:21326000-21361000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:21326800-21361800	Weak transcription	Stomach Mucosa	stomach
6	chr19:21327000-21347000	Weak transcription	Hela-S3	cervix
7	chr19:21331000-21371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:21332800-21356400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:21333000-21350000	Weak transcription	Fetal Kidney	kidney
10	chr19:21333000-21373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:21333200-21347000	Weak transcription	Gastric	stomach
12	chr19:21333200-21357400	Weak transcription	Pancreas	Pancrea
13	chr19:21333400-21364800	Weak transcription	HUVEC	blood vessel
14	chr19:21334000-21344400	Weak transcription	Spleen	Spleen
15	chr19:21334600-21360800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:21335000-21365000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:21335800-21348200	Weak transcription	Brain Substantia Nigra	brain
18	chr19:21335800-21357000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:21335800-21362800	Weak transcription	Psoas Muscle	Psoas
20	chr19:21336000-21357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:21336000-21362000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:21336200-21344600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:21336200-21346000	Weak transcription	HSMMtube	muscle
24	chr19:21336200-21349800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:21336200-21349800	Weak transcription	Fetal Lung	lung
26	chr19:21336200-21350000	Weak transcription	Adipose Nuclei	Adipose
27	chr19:21336200-21350000	Weak transcription	Placenta	Placenta
28	chr19:21336200-21350400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:21336200-21351800	Weak transcription	Brain Anterior Caudate	brain
30	chr19:21336200-21352200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:21336200-21361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr19:21336200-21361800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr19:21336400-21344400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr19:21336400-21349400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:21336600-21360600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:21336800-21345800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:21337000-21357000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:21338200-21347600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:21338200-21354400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:21338400-21347200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:21338600-21347800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr19:21338800-21344400	Weak transcription	Esophagus	oesophagus
43	chr19:21339000-21348400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:21339200-21344400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:21339200-21344800	Weak transcription	Lung	lung
46	chr19:21339200-21345000	Weak transcription	HepG2	liver
47	chr19:21339200-21346000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:21339200-21346400	Weak transcription	Left Ventricle	heart
49	chr19:21339200-21349000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:21339200-21354200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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