Variant report

Variant	rs10001493
Chromosome Location	chr4:106818592-106818593
allele	C/G
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	CTCF	chr4:106818580-106818730	MCF-7	breast:	n/a	n/a
2	FOS	chr4:106818519-106818906	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr4:106816618-106818819	MCF-7	breast:	n/a	chr4:106818035-106818047 chr4:106818036-106818045 chr4:106818038-106818045 chr4:106818036-106818046
4	RUNX3	chr4:106818501-106818970	GM12878	blood:	n/a	n/a
5	FOS	chr4:106818522-106818803	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr4:106818506-106818855	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr4:106817686-106818597	MCF-7	breast:	n/a	chr4:106818035-106818047 chr4:106818036-106818045 chr4:106818038-106818045 chr4:106818036-106818046
8	FOXM1	chr4:106818554-106818900	GM12878	blood:	n/a	n/a
9	SIN3AK20	chr4:106815818-106818678	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106817938..106820838-chr4:106829455..106833276,3	MCF-7	breast:
2	chr4:106393662..106395828-chr4:106816451..106818779,3	MCF-7	breast:

Variant related genes	Relation type
NPNT	TF binding region
INTS12	TF binding region
ENSG00000138777	Chromatin interaction
ENSG00000168743	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10000995	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10004951	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10006990	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10007955	0.82[YRI][hapmap]
rs10008593	0.91[EUR][1000 genomes]
rs10013403	0.97[EUR][1000 genomes]
rs10027191	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10033978	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10470990	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11726457	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11731982	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17036356	0.97[EUR][1000 genomes]
rs17036363	0.97[EUR][1000 genomes]
rs28369208	0.97[EUR][1000 genomes]
rs28465019	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28481382	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28544485	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28557167	0.91[EUR][1000 genomes]
rs6850909	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73839049	0.97[EUR][1000 genomes]
rs9992491	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106815800-106818600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:106815800-106818600	Active TSS	GM12878-XiMat	blood
3	chr4:106815800-106819200	Active TSS	Aorta	Aorta
4	chr4:106816000-106818800	Active TSS	Fetal Intestine Small	intestine
5	chr4:106816600-106818600	Bivalent/Poised TSS	HSMMtube	muscle
6	chr4:106817000-106819200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:106817000-106819200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
8	chr4:106817600-106818800	Bivalent/Poised TSS	Fetal Kidney	kidney
9	chr4:106818000-106819000	Weak transcription	Pancreas	Pancrea
10	chr4:106818000-106819200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr4:106818000-106819400	Bivalent Enhancer	HepG2	liver
12	chr4:106818000-106824400	Weak transcription	Small Intestine	intestine
13	chr4:106818000-106844800	Weak transcription	Psoas Muscle	Psoas
14	chr4:106818200-106818800	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:106818200-106818800	Bivalent Enhancer	Fetal Lung	lung
16	chr4:106818200-106819400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:106818200-106819400	Enhancers	Duodenum Mucosa	Duodenum
18	chr4:106818200-106819400	Enhancers	Hela-S3	cervix
19	chr4:106818200-106819400	Enhancers	NHEK	skin
20	chr4:106818200-106820200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr4:106818200-106830400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:106818400-106818600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:106818400-106818800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
24	chr4:106818400-106818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:106818400-106819400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr4:106818400-106819600	Enhancers	Fetal Heart	heart

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