Variant report

Variant	rs7250258
Chromosome Location	chr19:19977273-19977274
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19975991..19979508-chr19:19981059..19984923,4	K562	blood:
2	chr19:19976218..19978192-chr19:20011161..20013662,4	K562	blood:
3	chr19:19857732..19859328-chr19:19976906..19978604,2	MCF-7	breast:
4	chr19:19966687..19968532-chr19:19975349..19978266,2	MCF-7	breast:
5	chr19:19779650..19782100-chr19:19976513..19978467,2	MCF-7	breast:
6	chr19:19976692..19979119-chr19:20011140..20013486,2	K562	blood:

Variant related genes	Relation type
ENSG00000181896	Chromatin interaction
ENSG00000270270	Chromatin interaction
ENSG00000270325	Chromatin interaction
ENSG00000267268	Chromatin interaction
ENSG00000184635	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10415754	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10421280	0.82[AFR][1000 genomes]
rs1469700	0.82[AFR][1000 genomes]
rs1469701	0.81[AFR][1000 genomes]
rs1469702	0.81[AFR][1000 genomes]
rs2116888	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304169	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28888982	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3926422	0.81[AFR][1000 genomes]
rs4808221	0.86[AFR][1000 genomes]
rs4809002	0.86[AFR][1000 genomes]
rs4809003	0.86[AFR][1000 genomes]
rs66624169	0.86[AFR][1000 genomes]
rs7252427	0.86[AFR][1000 genomes]
rs7260247	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7250258	ZNF253	cis	Nerve Tibial	GTEx
rs7250258	ZNF682	cis	Muscle Skeletal	GTEx
rs7250258	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19975800-19978400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:19975800-19978400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:19975800-19978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:19976000-19977400	Active TSS	NHEK	skin
5	chr19:19976000-19977600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:19976000-19977600	Active TSS	Osteobl	bone
7	chr19:19976000-19978000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:19976000-19978200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr19:19976000-19978200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:19976000-19978200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr19:19976000-19978400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:19976000-19978400	Active TSS	Rectal Smooth Muscle	rectum
13	chr19:19976000-19978400	Active TSS	HMEC	breast
14	chr19:19976000-19978600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:19976000-19978600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr19:19976000-19978600	Active TSS	Colon Smooth Muscle	Colon
17	chr19:19976000-19978800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:19976000-19978800	Active TSS	Duodenum Mucosa	Duodenum
19	chr19:19976000-19979000	Active TSS	Brain Angular Gyrus	brain
20	chr19:19976000-19979200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr19:19976000-19979200	Active TSS	Right Atrium	heart
22	chr19:19976200-19977400	Active TSS	Primary hematopoietic stem cells	blood
23	chr19:19976200-19977600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:19976200-19977600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:19976200-19977600	Active TSS	Adipose Nuclei	Adipose
26	chr19:19976200-19977600	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr19:19976200-19978000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:19976200-19978000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:19976200-19978200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr19:19976200-19978200	Active TSS	Brain Hippocampus Middle	brain
31	chr19:19976200-19978200	Active TSS	Brain Substantia Nigra	brain
32	chr19:19976200-19978200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr19:19976200-19978600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:19976200-19978600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:19976200-19978600	Active TSS	Fetal Stomach	stomach
36	chr19:19976200-19978600	Active TSS	Right Ventricle	heart
37	chr19:19976200-19979200	Active TSS	Brain Germinal Matrix	brain
38	chr19:19976200-19979200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr19:19976200-19979200	Active TSS	Stomach Smooth Muscle	stomach
40	chr19:19976400-19977400	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr19:19976400-19977400	Active TSS	Primary T cells fromperipheralblood	blood
42	chr19:19976400-19977400	Active TSS	Fetal Muscle Trunk	muscle
43	chr19:19976400-19977600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:19976400-19977600	Active TSS	Primary B cells from cord blood	blood
45	chr19:19976400-19977600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:19976400-19977600	Active TSS	Thymus	Thymus
47	chr19:19976400-19978000	Active TSS	Primary T cells from cord blood	blood
48	chr19:19976400-19978000	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr19:19976400-19978000	Active TSS	Dnd41	blood
50	chr19:19976400-19978000	Active TSS	HSMM	muscle

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