Variant report

Variant	rs4979493
Chromosome Location	chr9:117856554-117856555
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	chr9:117853634-117857758	U87	brain:	n/a	n/a
2	POLR2A	chr9:117851943-117857764	U87	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1250019	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1511	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1755639	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1757106	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1757107	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1819419	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274836	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2480930	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789867	0.80[EUR][1000 genomes]
rs3789868	0.80[EUR][1000 genomes]
rs944227	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
3	chr9:117849400-117856800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
5	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
7	chr9:117849600-117864600	Weak transcription	HMEC	breast
8	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:117850800-117857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:117852400-117857000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:117853200-117856600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:117853400-117857000	Weak transcription	NHLF	lung
15	chr9:117853400-117857200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:117853400-117857200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:117853400-117858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:117853400-117861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:117854000-117860600	Weak transcription	NHDF-Ad	bronchial
21	chr9:117854400-117860600	Weak transcription	Osteobl	bone
22	chr9:117855000-117857000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr9:117855200-117857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr9:117855200-117857200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr9:117855200-117857600	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:117855200-117861000	Weak transcription	NH-A	brain
27	chr9:117855400-117857200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr9:117855400-117857400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:117855400-117857600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr9:117855600-117856800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr9:117855600-117857200	Enhancers	Fetal Lung	lung
32	chr9:117855600-117857600	Enhancers	Colon Smooth Muscle	Colon
33	chr9:117855800-117856600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:117855800-117856600	Enhancers	Stomach Smooth Muscle	stomach
35	chr9:117855800-117856600	Strong transcription	NHEK	skin
36	chr9:117855800-117857200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:117856000-117856600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr9:117856000-117856800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:117856000-117856800	Enhancers	Fetal Stomach	stomach
40	chr9:117856200-117856800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:117856200-117857200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:117856200-117857400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:117856400-117857000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:117856400-117857200	Enhancers	Brain Substantia Nigra	brain
45	chr9:117856400-117857400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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