Variant report

Variant	rs9496362
Chromosome Location	chr6:142709830-142709831
allele	A/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	MAX	chr6:142709456-142709835	A549	lung:	n/a	n/a
2	SMC3	chr6:142709169-142709975	SK-N-SH	brain:	n/a	chr6:142709541-142709555
3	RAD21	chr6:142709028-142709835	HepG2	liver:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
4	CTCF	chr6:142709760-142709910	AG09309	skin:	n/a	n/a
5	RAD21	chr6:142709219-142709843	A549	lung:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
6	CTCF	chr6:142709820-142709970	AG09319	gingival:	n/a	n/a
7	CTCF	chr6:142709780-142709930	GM12873	blood:	n/a	n/a
8	CTCF	chr6:142709153-142709930	SK-N-SH	brain:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
9	RAD21	chr6:142709169-142709860	HCT-116	colon:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
10	RAD21	chr6:142709258-142709900	HCT-116	colon:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
11	RAD21	chr6:142709157-142709955	SK-N-SH	brain:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
12	SMC3	chr6:142709265-142709918	Hela-S3	cervix:	n/a	chr6:142709541-142709555
13	CTCF	chr6:142709203-142710048	A549	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
14	CTCF	chr6:142709740-142709890	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:142477371..142478101-chr6:142709070..142709995,3	K562	blood:
2	chr6:142596671..142598809-chr6:142708125..142710238,2	MCF-7	breast:
3	chr6:142467634..142468596-chr6:142709170..142710030,4	MCF-7	breast:
4	chr6:142621739..142624319-chr6:142709513..142711217,3	MCF-7	breast:
5	chr6:142466930..142469707-chr6:142709065..142710643,2	K562	blood:
6	chr6:142528358..142528953-chr6:142709482..142710029,2	MCF-7	breast:
7	chr6:142616281..142618889-chr6:142707145..142709982,2	MCF-7	breast:

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000009844	Chromatin interaction
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13437156	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1411147	1.00[AMR][1000 genomes]
rs6921559	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484629	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484635	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484636	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484638	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484640	1.00[AMR][1000 genomes]
rs9484641	1.00[AMR][1000 genomes]
rs9484644	1.00[AMR][1000 genomes]
rs9496336	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496350	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496351	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496363	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496375	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496376	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496381	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496383	1.00[AMR][1000 genomes]
rs9496384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496385	1.00[AMR][1000 genomes]
rs9496386	1.00[AMR][1000 genomes]
rs9496387	1.00[AMR][1000 genomes]
rs9496393	1.00[AMR][1000 genomes]
rs9496407	1.00[AMR][1000 genomes]
rs9496408	1.00[AMR][1000 genomes]
rs9496410	1.00[AMR][1000 genomes]

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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:142700000-142714200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:142705800-142713800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:142706200-142719600	Weak transcription	NHEK	skin
7	chr6:142706400-142717200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:142706600-142710200	Enhancers	A549	lung
9	chr6:142708000-142710000	Enhancers	Liver	Liver
10	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
11	chr6:142708200-142710000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:142708200-142710000	Enhancers	NHLF	lung
13	chr6:142708200-142718600	Weak transcription	Placenta	Placenta
14	chr6:142708200-142719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:142708800-142711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:142709200-142710000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:142709200-142710000	Enhancers	HUVEC	blood vessel
18	chr6:142709200-142710600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:142709200-142721000	Weak transcription	Fetal Intestine Small	intestine
20	chr6:142709400-142711800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:142709400-142718800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:142709600-142710000	Enhancers	Primary T cells from cord blood	blood
23	chr6:142709800-142710000	Enhancers	Fetal Lung	lung
24	chr6:142709800-142710200	Enhancers	HSMM	muscle
25	chr6:142709800-142711400	Weak transcription	HepG2	liver

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