Variant report

Variant	rs6477844
Chromosome Location	chr9:99802351-99802352
allele	A/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	MXI1	chr9:99800582-99802370	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:99801409-99802675	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99636633..99638588-chr9:99800511..99803120,2	MCF-7	breast:

Variant related genes	Relation type
CTSV	TF binding region
ENSG00000196597	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10114720	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10115220	0.83[EUR][1000 genomes]
rs10118886	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118923	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739296	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759389	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10759391	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10759399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759400	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759406	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759417	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759420	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816926	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816951	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816953	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816962	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10816963	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816964	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816981	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816994	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817013	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10980241	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10980243	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10980326	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10980346	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10980396	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12236690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12376012	0.83[ASN][1000 genomes]
rs12376575	0.85[ASN][1000 genomes]
rs12377546	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs15394	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16919034	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16924211	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2004336	0.84[ASN][1000 genomes]
rs34342973	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4367680	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4501700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4510972	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59995818	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62560873	0.82[ASN][1000 genomes]
rs7023974	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7035822	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7038926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7039198	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7857836	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7875800	0.92[CEU][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9792463	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053215	chr9:99483926-99824810	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1824305	chr9:99792208-99806169	Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1821221	chr9:99792208-99811206	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99800400-99802400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:99800800-99802400	Active TSS	A549	lung
3	chr9:99801000-99802400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:99801200-99802400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:99802000-99802400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:99802000-99802400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:99802000-99802400	Enhancers	Placenta	Placenta
8	chr9:99802000-99802400	Bivalent Enhancer	Fetal Stomach	stomach
9	chr9:99802000-99802400	Enhancers	Stomach Mucosa	stomach
10	chr9:99802000-99803600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:99802000-99804200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:99802000-99807200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:99802000-99807600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:99802000-99808400	Weak transcription	Pancreas	Pancrea
15	chr9:99802200-99802400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:99802200-99802400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:99802200-99802400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:99802200-99802400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:99802200-99802400	Enhancers	Fetal Intestine Small	intestine
20	chr9:99802200-99802400	Enhancers	HMEC	breast
21	chr9:99802200-99802400	Enhancers	NHEK	skin
22	chr9:99802200-99802600	Enhancers	Fetal Intestine Large	intestine
23	chr9:99802200-99803000	Weak transcription	Brain Anterior Caudate	brain
24	chr9:99802200-99803600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:99802200-99804000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:99802200-99804000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:99802200-99804400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:99802200-99804400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:99802200-99807000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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