Variant report

Variant	rs2303010
Chromosome Location	chr5:179752031-179752032
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	chr5:179750833-179752935	U87	brain:	n/a	n/a
2	POLR2A	chr5:179751932-179752459	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179751754-179752124	U87	brain:	n/a	n/a
4	POLR2A	chr5:179751573-179752739	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179751622-179752321	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:179751949-179752349	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:179750839-179752549	U87	brain:	n/a	n/a

Variant related genes	Relation type
GFPT2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12654592	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs12655822	0.81[ASN][1000 genomes]
rs2042224	0.84[ASN][1000 genomes]
rs4323198	0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs55824010	0.98[ASN][1000 genomes]
rs60396605	0.84[ASN][1000 genomes]
rs60634512	0.84[ASN][1000 genomes]
rs73349659	0.84[ASN][1000 genomes]
rs73349662	0.84[ASN][1000 genomes]
rs73349695	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7447624	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
2	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
9	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
10	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:179740400-179757400	Weak transcription	NHLF	lung
14	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr5:179741200-179754000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179741600-179756000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:179741600-179757600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:179741800-179758200	Weak transcription	Fetal Intestine Small	intestine
20	chr5:179742000-179757400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179742600-179757800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
23	chr5:179743400-179754200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:179743400-179758200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:179743800-179756400	Weak transcription	Colonic Mucosa	Colon
26	chr5:179743800-179757400	Weak transcription	Fetal Lung	lung
27	chr5:179744000-179766600	Weak transcription	Gastric	stomach
28	chr5:179746000-179760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
30	chr5:179748200-179752800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179748400-179753200	Strong transcription	Fetal Stomach	stomach
32	chr5:179749200-179757400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:179750000-179752600	Weak transcription	Fetal Heart	heart
34	chr5:179750200-179752400	Enhancers	Brain Hippocampus Middle	brain
35	chr5:179750200-179752600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:179750200-179752600	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr5:179750200-179752800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:179750200-179756600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:179750200-179757400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:179750400-179752200	Genic enhancers	NH-A	brain
41	chr5:179750400-179752400	Enhancers	Brain Germinal Matrix	brain
42	chr5:179750400-179752400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr5:179750600-179752200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:179750600-179752200	Enhancers	Brain Anterior Caudate	brain
45	chr5:179750800-179752200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:179750800-179752200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:179750800-179752200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:179750800-179752400	Enhancers	Brain Substantia Nigra	brain
49	chr5:179751000-179752200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:179751000-179752400	Enhancers	Fetal Brain Male	brain

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