Variant report

Variant	rs7719940
Chromosome Location	chr5:16852734-16852735
allele	C/T
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	POLR2A	chr5:16852615-16853052	A549	lung:	n/a	n/a
2	EP300	chr5:16852556-16852849	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP179	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11133865	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625206	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4702175	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736840	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9312938	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv1026773	chr5:16846836-16877367	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16820800-16855200	Weak transcription	HSMM	muscle
2	chr5:16829400-16855800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:16832400-16855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:16834800-16853400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:16838200-16853600	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:16839000-16853000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:16839000-16855800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:16839000-16864600	Weak transcription	Fetal Brain Female	brain
9	chr5:16841800-16855600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:16842400-16862800	Weak transcription	Stomach Mucosa	stomach
11	chr5:16842600-16855200	Weak transcription	HUVEC	blood vessel
12	chr5:16842600-16855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:16843400-16855000	Weak transcription	Lung	lung
14	chr5:16843600-16852800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:16843600-16853600	Weak transcription	HSMMtube	muscle
16	chr5:16844400-16855600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:16844800-16855600	Weak transcription	NHEK	skin
18	chr5:16845600-16857000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:16846400-16852800	Weak transcription	Small Intestine	intestine
20	chr5:16846800-16855600	Weak transcription	Gastric	stomach
21	chr5:16846800-16856200	Weak transcription	HMEC	breast
22	chr5:16847000-16855000	Weak transcription	Pancreas	Pancrea
23	chr5:16847000-16855600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:16847800-16856000	Weak transcription	Fetal Thymus	thymus
25	chr5:16848800-16855800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:16850000-16855800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:16850400-16855600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:16851200-16854400	Genic enhancers	A549	lung
29	chr5:16852200-16852800	Enhancers	Fetal Kidney	kidney
30	chr5:16852200-16853000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:16852200-16853000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:16852200-16856400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr5:16852400-16852800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:16852400-16853000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:16852400-16853200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:16852400-16853200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr5:16852400-16853200	Enhancers	Fetal Stomach	stomach
38	chr5:16852400-16853600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:16852400-16854000	Enhancers	NHDF-Ad	bronchial
40	chr5:16852400-16858200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:16852600-16852800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:16852600-16852800	Enhancers	Fetal Intestine Large	intestine
43	chr5:16852600-16852800	Weak transcription	NHLF	lung
44	chr5:16852600-16853000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr5:16852600-16853000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:16852600-16853000	Enhancers	Fetal Lung	lung
47	chr5:16852600-16853000	Enhancers	NH-A	brain
48	chr5:16852600-16853200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:16852600-16853200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:16852600-16853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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