Variant report

Variant	rs7258260
Chromosome Location	chr19:20040475-20040476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1019279	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10403255	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10407726	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10408752	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10412710	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10414919	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10415179	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10426937	0.87[EUR][1000 genomes]
rs1048421	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13344370	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2060239	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2160156	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2335365	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2335366	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2335368	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28590063	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3943792	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809006	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809016	0.87[ASN][1000 genomes]
rs55816500	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60765256	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511058	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511059	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66970424	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246569	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252079	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253407	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7254355	0.87[EUR][1000 genomes]
rs7256224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73532705	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8105329	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105482	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108528	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109743	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113576	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8113694	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv1056595	chr19:20020626-20061367	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv458376	chr19:20021046-20151257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv578800	chr19:20021046-20151257	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv911319	chr19:20025940-20170214	ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7258260	ZNF93	cis	Thyroid	GTEx
rs7258260	ZNF253	cis	Nerve Tibial	GTEx
rs7258260	ZNF682	cis	Muscle Skeletal	GTEx
rs7258260	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20012800-20043400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:20013200-20043600	Weak transcription	Fetal Brain Male	brain
3	chr19:20027600-20043200	Weak transcription	HSMMtube	muscle
4	chr19:20032000-20046800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr19:20032600-20042800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:20032600-20046400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:20032600-20046800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:20032600-20047000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:20032600-20047000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:20032800-20046600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:20033400-20040600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:20033400-20044200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:20033400-20046400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:20033400-20046600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:20033400-20047000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:20033400-20047800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:20033600-20045600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:20033800-20044600	Weak transcription	Brain Anterior Caudate	brain
19	chr19:20034000-20040600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:20034000-20044400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr19:20034000-20046000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:20034000-20046400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:20034000-20046600	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:20034000-20047000	ZNF genes & repeats	Dnd41	blood
25	chr19:20034200-20041400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
26	chr19:20034200-20046000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:20034200-20046400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
28	chr19:20034800-20045600	Weak transcription	Pancreas	Pancrea
29	chr19:20035000-20044000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:20035000-20044400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:20036000-20040600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:20036000-20044600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:20036200-20041200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:20036200-20044400	Weak transcription	Left Ventricle	heart
35	chr19:20036200-20044400	Weak transcription	Ovary	ovary
36	chr19:20037000-20046400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
37	chr19:20037200-20042200	Weak transcription	Psoas Muscle	Psoas
38	chr19:20037800-20042800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:20038000-20043400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:20038200-20044400	Weak transcription	Stomach Mucosa	stomach
41	chr19:20038400-20042000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:20038600-20044000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:20038800-20041000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:20038800-20041200	Weak transcription	Adipose Nuclei	Adipose
45	chr19:20038800-20042200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:20038800-20042800	Weak transcription	Placenta	Placenta
47	chr19:20039000-20041000	Weak transcription	Fetal Thymus	thymus
48	chr19:20039600-20043000	Weak transcription	Osteobl	bone
49	chr19:20039800-20043200	Weak transcription	NHDF-Ad	bronchial
50	chr19:20040000-20041000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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