Variant report

Variant	rs3747680
Chromosome Location	chr4:85612737-85612738
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	FOS	chr4:85612110-85613172	MCF10A-Er-Src	breast:	n/a	chr4:85612787-85612798 chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612443 chr4:85612433-85612442
2	POLR2A	chr4:85612607-85612866	HUVEC	blood vessel:	n/a	n/a
3	FOSL2	chr4:85612614-85612933	A549	lung:	n/a	n/a
4	TCF7L2	chr4:85612283-85612962	PANC-1	pancreas:	n/a	chr4:85612432-85612441 chr4:85612433-85612442
5	SP1	chr4:85612048-85613207	HCT-116	colon:	n/a	n/a
6	POLR2A	chr4:85612202-85612966	U87	brain:	n/a	n/a
7	FOS	chr4:85612017-85613048	MCF10A-Er-Src	breast:	n/a	chr4:85612787-85612798 chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612443 chr4:85612433-85612442
8	CEBPB	chr4:85612057-85613159	HCT-116	colon:	n/a	n/a
9	JUND	chr4:85612059-85613144	SK-N-SH	brain:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
10	TCF12	chr4:85612068-85613136	SK-N-SH	brain:	n/a	n/a
11	JUND	chr4:85612251-85612940	Hela-S3	cervix:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
12	MYC	chr4:85612391-85612958	MCF10A-Er-Src	breast:	n/a	chr4:85612433-85612442
13	CEBPB	chr4:85612131-85612942	IMR90	lung:	n/a	n/a
14	EP300	chr4:85612193-85612932	SK-N-SH_RA	brain:	n/a	chr4:85612433-85612442
15	POLR2A	chr4:85612202-85613015	U87	brain:	n/a	n/a
16	RFX5	chr4:85612463-85612837	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr4:85612347-85612976	MCF10A-Er-Src	breast:	n/a	chr4:85612764-85612772 chr4:85612432-85612441
18	JUND	chr4:85611994-85613157	SK-N-SH	brain:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
19	GATA3	chr4:85612011-85613165	SK-N-SH	brain:	n/a	chr4:85612766-85612776
20	FOS	chr4:85612237-85613043	MCF10A-Er-Src	breast:	n/a	chr4:85612787-85612798 chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612443 chr4:85612433-85612442
21	TCF12	chr4:85611990-85613151	SK-N-SH	brain:	n/a	n/a
22	E2F4	chr4:85612387-85612752	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr4:85612459-85612914	PANC-1	pancreas:	n/a	n/a
24	EP300	chr4:85612226-85613182	SK-N-SH	brain:	n/a	chr4:85612433-85612442
25	MAFK	chr4:85612253-85612904	IMR90	lung:	n/a	chr4:85612466-85612477 chr4:85612467-85612478 chr4:85612466-85612477 chr4:85612434-85612443
26	ATF3	chr4:85612168-85613076	HCT-116	colon:	n/a	n/a
27	STAT3	chr4:85612598-85612914	Hela-S3	cervix:	n/a	chr4:85612764-85612772
28	POLR2A	chr4:85612273-85612962	HCT-116	colon:	n/a	n/a
29	SRF	chr4:85612140-85613089	HCT-116	colon:	n/a	n/a
30	JUND	chr4:85612359-85612831	H1-hESC	embryonic stem cell:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
31	EGR1	chr4:85612339-85613055	HCT-116	colon:	n/a	n/a
32	SP1	chr4:85612484-85612909	A549	lung:	n/a	n/a
33	JUND	chr4:85612264-85612781	HepG2	liver:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
34	CEBPB	chr4:85612205-85612967	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr4:85612347-85612771	Hela-S3	cervix:	n/a	n/a
36	FOS	chr4:85612305-85612980	Hela-S3	cervix:	n/a	chr4:85612787-85612798 chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612443 chr4:85612433-85612442
37	GATA3	chr4:85612132-85613065	SK-N-SH	brain:	n/a	chr4:85612766-85612776
38	SP1	chr4:85612063-85613163	HCT-116	colon:	n/a	n/a
39	POLR2A	chr4:85612400-85612976	MCF10A-Er-Src	breast:	n/a	n/a
40	GATA3	chr4:85612362-85613014	A549	lung:	n/a	chr4:85612766-85612776
41	NFIC	chr4:85612081-85613151	SK-N-SH	brain:	n/a	n/a
42	GTF2F1	chr4:85612419-85612802	Hela-S3	cervix:	n/a	n/a
43	MYC	chr4:85612387-85612891	MCF10A-Er-Src	breast:	n/a	chr4:85612433-85612442
44	PBX3	chr4:85612131-85613041	SK-N-SH	brain:	n/a	n/a
45	JUND	chr4:85612022-85613111	HCT-116	colon:	n/a	chr4:85612432-85612441 chr4:85612432-85612442 chr4:85612431-85612442 chr4:85612431-85612443 chr4:85612433-85612442
46	MAX	chr4:85611544-85612930	NB4	blood:	n/a	chr4:85612433-85612442
47	TEAD4	chr4:85612209-85613142	SK-N-SH	brain:	n/a	chr4:85613113-85613122
48	NFIC	chr4:85612190-85613024	SK-N-SH	brain:	n/a	n/a
49	EP300	chr4:85612052-85613174	SK-N-SH	brain:	n/a	chr4:85612433-85612442
50	MEF2A	chr4:85612161-85612926	SK-N-SH	brain:	n/a	chr4:85612768-85612776 chr4:85612433-85612441

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:85503764..85505727-chr4:85612684..85615116,2	K562	blood:

Variant related genes	Relation type
RN7SL552P	TF binding region
ENSG00000163624	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11725121	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12502294	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12502409	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12511112	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13118671	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs1484661	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16995920	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17009317	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs17009334	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2218323	0.89[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs36036245	0.88[ASN][1000 genomes]
rs6816534	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6825852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6829807	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs6838727	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6858666	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs7685537	0.87[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3747680	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85587800-85648400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:85592200-85613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85596200-85634600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:85598600-85632800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:85602600-85630600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:85603400-85618600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr4:85603400-85631600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:85603600-85618400	Strong transcription	Liver	Liver
9	chr4:85603800-85643800	Weak transcription	Stomach Mucosa	stomach
10	chr4:85604400-85618400	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:85604400-85637600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
13	chr4:85604800-85631600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:85605000-85637000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:85605200-85616000	Weak transcription	Colonic Mucosa	Colon
16	chr4:85605200-85616200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:85605400-85615400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:85605800-85616200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:85606600-85616600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:85607000-85615600	Weak transcription	Fetal Brain Male	brain
21	chr4:85607000-85619200	Strong transcription	Fetal Kidney	kidney
22	chr4:85607800-85636000	Strong transcription	Fetal Lung	lung
23	chr4:85608600-85618000	Strong transcription	Brain Germinal Matrix	brain
24	chr4:85609000-85618600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:85609200-85627400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:85609600-85614000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:85609800-85612800	Weak transcription	Brain Angular Gyrus	brain
28	chr4:85609800-85623400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:85610200-85616000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:85610600-85618400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr4:85611000-85617200	Strong transcription	Fetal Intestine Large	intestine
32	chr4:85611400-85614200	Strong transcription	Left Ventricle	heart
33	chr4:85611400-85614600	Genic enhancers	HUVEC	blood vessel
34	chr4:85611400-85618600	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:85611600-85612800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr4:85611600-85612800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr4:85611600-85613400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:85611600-85613400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:85611600-85613400	Genic enhancers	Primary monocytes fromperipheralblood	blood
40	chr4:85611600-85613400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:85611600-85613400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:85611600-85613400	Genic enhancers	Placenta	Placenta
43	chr4:85611600-85613400	Strong transcription	Ovary	ovary
44	chr4:85611600-85613600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:85611600-85613600	Strong transcription	Lung	lung
46	chr4:85611600-85613600	Strong transcription	Pancreas	Pancrea
47	chr4:85611600-85613600	Strong transcription	Spleen	Spleen
48	chr4:85611600-85613800	Strong transcription	Fetal Intestine Small	intestine
49	chr4:85611600-85614000	Strong transcription	Fetal Stomach	stomach
50	chr4:85611600-85614400	Strong transcription	HepG2	liver

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