Variant report

Variant	rs10415754
Chromosome Location	chr19:19976221-19976222
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr19:19976200-19977933	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr19:19976118-19976281	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:19976142-19976267	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:19976008-19976251	HepG2	liver:	n/a	n/a

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	chr19:19966687..19968532-chr19:19975349..19978266,2	MCF-7	breast:

Variant related genes	Relation type
ZNF253	TF binding region
ENSG00000270270	Chromatin interaction
ENSG00000270325	Chromatin interaction
ENSG00000184635	Chromatin interaction
ENSG00000267268	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2116888	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304169	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28888982	0.82[EUR][1000 genomes]
rs7250258	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10415754	ZNF253	cis	Nerve Tibial	GTEx
rs10415754	ZNF682	cis	Muscle Skeletal	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19972000-19976600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:19972200-19976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:19972200-19976600	Weak transcription	Spleen	Spleen
4	chr19:19973800-19976600	Weak transcription	HepG2	liver
5	chr19:19975800-19978400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19975800-19978400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr19:19975800-19978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:19976000-19976400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr19:19976000-19976400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr19:19976000-19976400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:19976000-19976400	Flanking Active TSS	Liver	Liver
12	chr19:19976000-19976400	Enhancers	Esophagus	oesophagus
13	chr19:19976000-19976600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr19:19976000-19976600	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:19976000-19976800	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:19976000-19977200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:19976000-19977400	Active TSS	NHEK	skin
18	chr19:19976000-19977600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:19976000-19977600	Active TSS	Osteobl	bone
20	chr19:19976000-19978000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19976000-19978200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr19:19976000-19978200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:19976000-19978200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr19:19976000-19978400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:19976000-19978400	Active TSS	Rectal Smooth Muscle	rectum
26	chr19:19976000-19978400	Active TSS	HMEC	breast
27	chr19:19976000-19978600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:19976000-19978600	Active TSS	Muscle Satellite Cultured Cells	--
29	chr19:19976000-19978600	Active TSS	Colon Smooth Muscle	Colon
30	chr19:19976000-19978800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:19976000-19978800	Active TSS	Duodenum Mucosa	Duodenum
32	chr19:19976000-19979000	Active TSS	Brain Angular Gyrus	brain
33	chr19:19976000-19979200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:19976000-19979200	Active TSS	Right Atrium	heart
35	chr19:19976200-19976400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:19976200-19976400	Enhancers	Dnd41	blood
37	chr19:19976200-19976600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:19976200-19976600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:19976200-19976600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:19976200-19976600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:19976200-19976600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:19976200-19976600	Weak transcription	Placenta	Placenta
43	chr19:19976200-19976600	Weak transcription	Pancreas	Pancrea
44	chr19:19976200-19977000	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:19976200-19977400	Active TSS	Primary hematopoietic stem cells	blood
46	chr19:19976200-19977600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:19976200-19977600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:19976200-19977600	Active TSS	Adipose Nuclei	Adipose
49	chr19:19976200-19977600	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:19976200-19978000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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