Variant report

Variant	rs2546194
Chromosome Location	chr5:95193312-95193313
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	chr5:95192953-95193405	HUVEC	blood vessel:	n/a	n/a
2	E2F6	chr5:95193149-95193478	K562	blood:	n/a	chr5:95193344-95193351 chr5:95193341-95193352 chr5:95193344-95193351 chr5:95193344-95193351
3	NFIC	chr5:95192958-95193473	HepG2	liver:	n/a	n/a
4	RCOR1	chr5:95192845-95193336	HepG2	liver:	n/a	n/a
5	NR2F2	chr5:95192819-95193495	K562	blood:	n/a	n/a
6	RFX5	chr5:95192942-95193357	HepG2	liver:	n/a	n/a
7	TCF7L2	chr5:95193158-95193518	HepG2	liver:	n/a	chr5:95193318-95193327 chr5:95193319-95193328
8	FOXA1	chr5:95192866-95193523	HepG2	liver:	n/a	n/a
9	FOXA1	chr5:95192965-95193333	A549	lung:	n/a	n/a
10	EP300	chr5:95192845-95193491	HepG2	liver:	n/a	n/a
11	REST	chr5:95192957-95193444	HepG2	liver:	n/a	n/a
12	NR3C1	chr5:95192804-95193461	A549	lung:	n/a	chr5:95193188-95193202 chr5:95193318-95193327 chr5:95193188-95193202 chr5:95193074-95193087 chr5:95193188-95193202 chr5:95193153-95193179 chr5:95193166-95193173
13	HNF4A	chr5:95192949-95193359	HepG2	liver:	n/a	chr5:95193175-95193187 chr5:95193174-95193188 chr5:95193172-95193190 chr5:95193175-95193187 chr5:95193175-95193187 chr5:95193173-95193188 chr5:95193175-95193188 chr5:95193170-95193192 chr5:95193174-95193187 chr5:95193175-95193187
14	USF1	chr5:95193168-95193407	HepG2	liver:	n/a	n/a
15	FOXA1	chr5:95192870-95193380	HepG2	liver:	n/a	n/a
16	SP1	chr5:95192871-95193449	HepG2	liver:	n/a	n/a
17	FOSL2	chr5:95192968-95193513	HepG2	liver:	n/a	chr5:95193316-95193324 chr5:95193318-95193327
18	E2F6	chr5:95193153-95193572	H1-hESC	embryonic stem cell:	n/a	chr5:95193344-95193351 chr5:95193341-95193352 chr5:95193344-95193351 chr5:95193344-95193351
19	JUND	chr5:95193099-95193398	HepG2	liver:	n/a	chr5:95193316-95193324 chr5:95193318-95193327 chr5:95193317-95193328
20	MAX	chr5:95192896-95193501	HUVEC	blood vessel:	n/a	chr5:95193307-95193316
21	CBX3	chr5:95193007-95193466	K562	blood:	n/a	n/a
22	MBD4	chr5:95192899-95193535	HepG2	liver:	n/a	n/a
23	FOS	chr5:95193059-95193571	HUVEC	blood vessel:	n/a	chr5:95193316-95193324 chr5:95193318-95193327 chr5:95193317-95193328
24	ELF1	chr5:95193051-95193322	K562	blood:	n/a	n/a
25	POLR2A	chr5:95193203-95198379	IMR90	lung:	n/a	n/a
26	MAX	chr5:95193179-95193434	K562	blood:	n/a	chr5:95193307-95193316
27	FOS	chr5:95193247-95193361	MCF10A-Er-Src	breast:	n/a	chr5:95193316-95193324 chr5:95193318-95193327 chr5:95193317-95193328
28	MBD4	chr5:95192672-95193509	HepG2	liver:	n/a	n/a
29	NR3C1	chr5:95193023-95193392	A549	lung:	n/a	chr5:95193188-95193202 chr5:95193318-95193327 chr5:95193188-95193202 chr5:95193074-95193087 chr5:95193188-95193202 chr5:95193153-95193179 chr5:95193166-95193173
30	EP300	chr5:95192830-95193336	HepG2	liver:	n/a	n/a
31	TEAD4	chr5:95192743-95193492	HepG2	liver:	n/a	chr5:95192971-95192980
32	NR3C1	chr5:95192965-95193319	A549	lung:	n/a	chr5:95193188-95193202 chr5:95193188-95193202 chr5:95193074-95193087 chr5:95193188-95193202 chr5:95193153-95193179 chr5:95193166-95193173
33	MAX	chr5:95192874-95193530	HepG2	liver:	n/a	chr5:95193307-95193316
34	MAX	chr5:95192843-95193538	K562	blood:	n/a	chr5:95193307-95193316
35	MYBL2	chr5:95192959-95193575	HepG2	liver:	n/a	n/a
36	JUN	chr5:95193050-95193519	HUVEC	blood vessel:	n/a	chr5:95193316-95193324 chr5:95193318-95193327
37	POLR2A	chr5:95192801-95193510	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr5:95193003-95193376	HUVEC	blood vessel:	n/a	n/a
39	HDAC2	chr5:95192743-95193405	HepG2	liver:	n/a	n/a
40	JUND	chr5:95193195-95193343	K562	blood:	n/a	chr5:95193316-95193324 chr5:95193318-95193327 chr5:95193317-95193328
41	FOXA1	chr5:95192888-95193378	HepG2	liver:	n/a	n/a
42	TAL1	chr5:95192967-95193328	K562	blood:	n/a	n/a
43	JUND	chr5:95192968-95193496	HepG2	liver:	n/a	chr5:95193316-95193324 chr5:95193318-95193327 chr5:95193317-95193328
44	FOSL2	chr5:95193014-95193491	HepG2	liver:	n/a	chr5:95193316-95193324 chr5:95193318-95193327
45	USF1	chr5:95192923-95193439	HepG2	liver:	n/a	chr5:95193090-95193106
46	NR3C1	chr5:95192968-95193415	A549	lung:	n/a	chr5:95193188-95193202 chr5:95193318-95193327 chr5:95193188-95193202 chr5:95193074-95193087 chr5:95193188-95193202 chr5:95193153-95193179 chr5:95193166-95193173
47	NR3C1	chr5:95192872-95193402	A549	lung:	n/a	chr5:95193188-95193202 chr5:95193318-95193327 chr5:95193188-95193202 chr5:95193074-95193087 chr5:95193188-95193202 chr5:95193153-95193179 chr5:95193166-95193173
48	EP300	chr5:95192838-95193469	HepG2	liver:	n/a	n/a
49	MAX	chr5:95192757-95193763	HepG2	liver:	n/a	chr5:95193307-95193316
50	MAX	chr5:95192981-95193451	K562	blood:	n/a	chr5:95193307-95193316

No.	Distal block	Cell Line	Cell type
1	chr5:95187602..95189431-chr5:95191166..95193314,2	K562	blood:
2	chr5:95065746..95068516-chr5:95192441..95195088,2	K562	blood:
3	chr5:95191104..95193650-chr5:95201052..95202970,2	MCF-7	breast:
4	chr5:95192803..95195845-chr5:95402156..95405628,4	K562	blood:
5	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
6	chr5:95170114..95172338-chr5:95193145..95195226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251409	TF binding region
ENSG00000250362	TF binding region
ENSG00000250240	Chromatin interaction
ENSG00000251409	Chromatin interaction
ENSG00000251000	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000236882	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2161313	0.82[JPT][hapmap]
rs2546193	0.83[CHD][hapmap]
rs2547996	0.82[JPT][hapmap]
rs60868839	0.82[ASN][1000 genomes]
rs918469	0.82[JPT][hapmap]
rs918470	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95186400-95194200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:95188400-95195600	Enhancers	Fetal Heart	heart
4	chr5:95188600-95194400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:95189400-95193400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:95191000-95194200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:95191000-95194200	Enhancers	Brain Hippocampus Middle	brain
8	chr5:95191000-95194200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr5:95191000-95194200	Enhancers	Brain Substantia Nigra	brain
10	chr5:95191000-95194400	Enhancers	Brain Angular Gyrus	brain
11	chr5:95191200-95193400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:95191200-95194200	Enhancers	Brain Anterior Caudate	brain
13	chr5:95191200-95194200	Enhancers	Brain Cingulate Gyrus	brain
14	chr5:95191200-95194200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:95191800-95193600	Enhancers	Right Ventricle	heart
16	chr5:95191800-95194000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:95191800-95194400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:95191800-95195800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:95191800-95195800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:95192000-95201400	Enhancers	Placenta	Placenta
21	chr5:95192200-95193400	Weak transcription	Fetal Kidney	kidney
22	chr5:95192200-95193400	Enhancers	Fetal Muscle Trunk	muscle
23	chr5:95192200-95193400	Enhancers	HepG2	liver
24	chr5:95192200-95193600	Enhancers	NHLF	lung
25	chr5:95192200-95193800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:95192200-95194200	Enhancers	Adipose Nuclei	Adipose
27	chr5:95192200-95194200	Weak transcription	Fetal Brain Male	brain
28	chr5:95192200-95194400	Enhancers	Esophagus	oesophagus
29	chr5:95192200-95194400	Enhancers	Pancreas	Pancrea
30	chr5:95192200-95194400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr5:95192200-95194600	Enhancers	Left Ventricle	heart
32	chr5:95192200-95194600	Enhancers	Ovary	ovary
33	chr5:95192200-95194800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:95192200-95195000	Enhancers	Lung	lung
35	chr5:95192200-95195000	Enhancers	Right Atrium	heart
36	chr5:95192200-95195800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:95192200-95199400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:95192400-95193400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr5:95192400-95194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr5:95192400-95195400	Weak transcription	Small Intestine	intestine
41	chr5:95192400-95199200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr5:95192600-95193600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:95192600-95193800	Enhancers	Liver	Liver
44	chr5:95192800-95193400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:95192800-95193600	Enhancers	NHDF-Ad	bronchial
46	chr5:95192800-95193800	Enhancers	Hela-S3	cervix
47	chr5:95192800-95194200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:95192800-95194200	Enhancers	Aorta	Aorta
49	chr5:95192800-95194200	Enhancers	Colonic Mucosa	Colon
50	chr5:95192800-95194200	Enhancers	Colon Smooth Muscle	Colon

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