Variant report

Variant	rs7028990
Chromosome Location	chr9:97402623-97402624
allele	A/C
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	CTBP2	chr9:97402108-97403283	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr9:97400579-97402724	MCF-7	breast:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
3	MAX	chr9:97402025-97402668	H1-hESC	embryonic stem cell:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97402180-97402190
4	BACH1	chr9:97402359-97402724	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr9:97402303-97402686	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr9:97401229-97402727	H1-hESC	embryonic stem cell:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97401961-97401971 chr9:97402180-97402190 chr9:97401965-97401974
7	NANOG	chr9:97402330-97402726	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr9:97401850-97402686	H1-hESC	embryonic stem cell:	n/a	chr9:97401972-97401983
9	NANOG	chr9:97402403-97402688	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr9:97402427-97402782	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr9:97402246-97402685	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr9:97402021-97402647	H1-hESC	embryonic stem cell:	n/a	chr9:97402273-97402284 chr9:97402335-97402344 chr9:97402180-97402190
13	TCF12	chr9:97402282-97402738	H1-hESC	embryonic stem cell:	n/a	n/a
14	SUZ12	chr9:97400708-97402723	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97316754..97318987-chr9:97400777..97403144,3	MCF-7	breast:

Variant related genes	Relation type
FBP1	TF binding region
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10993270	0.90[CHB][hapmap]
rs12006206	0.86[CHB][hapmap]
rs12684841	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12685485	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910850	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16910853	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16910860	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28369691	0.89[EUR][1000 genomes]
rs28402377	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402378	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402384	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402386	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402389	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402390	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28402396	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28402397	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28402401	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28402404	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4111369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129219	0.86[CHB][hapmap]
rs4574908	0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs59327242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7019207	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035325	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73523269	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73523271	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849320	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850385	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867069	0.80[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97401000-97402800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:97401000-97402800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr9:97401000-97403000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:97401400-97402800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr9:97401600-97402800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr9:97401600-97403000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:97402000-97402800	Active TSS	HepG2	liver
8	chr9:97402200-97402800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr9:97402200-97402800	Enhancers	Small Intestine	intestine
10	chr9:97402200-97403000	Flanking Active TSS	Liver	Liver
11	chr9:97402200-97403000	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr9:97402200-97403000	Enhancers	Lung	lung
13	chr9:97402200-97403200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr9:97402200-97403400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:97402200-97410400	Weak transcription	Esophagus	oesophagus
16	chr9:97402400-97402800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr9:97402400-97402800	Enhancers	Primary B cells from cord blood	blood
18	chr9:97402400-97402800	Enhancers	Primary B cells from peripheral blood	blood
19	chr9:97402400-97402800	Enhancers	Primary hematopoietic stem cells	blood
20	chr9:97402400-97402800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr9:97402400-97402800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:97402400-97403000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr9:97402400-97403000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:97402400-97403000	Enhancers	Placenta	Placenta
25	chr9:97402400-97406600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr9:97402400-97420000	Weak transcription	Right Atrium	heart
27	chr9:97402600-97402800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:97402600-97402800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
29	chr9:97402600-97402800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:97402600-97402800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:97402600-97403000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr9:97402600-97403000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr9:97402600-97403000	Enhancers	Fetal Intestine Large	intestine
34	chr9:97402600-97403000	Enhancers	Pancreas	Pancrea
35	chr9:97402600-97403000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr9:97402600-97403200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr9:97402600-97403200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr9:97402600-97403200	Enhancers	Stomach Mucosa	stomach
39	chr9:97402600-97403400	Enhancers	Fetal Intestine Small	intestine
40	chr9:97402600-97403600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:97402600-97411000	Weak transcription	Gastric	stomach
42	chr9:97402600-97415400	Weak transcription	Spleen	Spleen

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