Variant report

Variant	rs4657
Chromosome Location	chr9:97849090-97849091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr9:97848569-97849108	A549	lung:	n/a	n/a
2	TCF12	chr9:97848215-97849456	A549	lung:	n/a	n/a
3	POLR2A	chr9:97847738-97849198	ECC-1	luminal epithelium:	n/a	n/a
4	FOSL2	chr9:97848831-97849252	A549	lung:	n/a	n/a
5	POLR2A	chr9:97848982-97849189	A549	lung:	n/a	n/a
6	POLR2A	chr9:97847662-97849192	A549	lung:	n/a	n/a
7	POLR2A	chr9:97848379-97849144	Hela-S3	cervix:	n/a	n/a
8	BCL3	chr9:97848950-97849520	A549	lung:	n/a	n/a
9	POLR2A	chr9:97848590-97849159	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr9:97849017-97849183	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr9:97848241-97849367	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:97848155-97849181	A549	lung:	n/a	n/a
13	MAZ	chr9:97849070-97849096	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr9:97846631-97849496	A549	lung:	n/a	n/a
15	POLR2A	chr9:97848982-97849202	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97542830..97545595-chr9:97848570..97851188,3	MCF-7	breast:
2	chr9:97848613..97851879-chr9:97854740..97857228,3	K562	blood:
3	chr9:97688794..97691032-chr9:97848721..97850468,2	MCF-7	breast:
4	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3074	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1011784	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739992	0.91[JPT][hapmap]
rs10761374	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821447	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821455	0.91[JPT][hapmap]
rs1979022	0.91[JPT][hapmap]
rs2166402	0.91[JPT][hapmap]
rs2297596	0.91[JPT][hapmap]
rs2297597	0.91[JPT][hapmap]
rs3277	0.91[JPT][hapmap]
rs3737142	0.91[JPT][hapmap]
rs3780564	0.91[JPT][hapmap]
rs3780568	0.91[JPT][hapmap]
rs3844341	0.91[JPT][hapmap]
rs3852402	0.91[JPT][hapmap]
rs4647459	0.91[JPT][hapmap]
rs4647462	0.91[JPT][hapmap]
rs4647475	0.91[JPT][hapmap]
rs4647528	0.91[JPT][hapmap]
rs4647554	0.91[JPT][hapmap];0.80[LWK][hapmap];0.83[MKK][hapmap];0.81[ASN][1000 genomes]
rs4647558	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4743988	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744442	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744446	0.91[JPT][hapmap]
rs6479598	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7033633	0.83[TSI][hapmap]
rs7034538	0.91[JPT][hapmap]
rs7042293	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7042320	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7046682	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850958	0.91[JPT][hapmap]
rs7854570	0.91[JPT][hapmap]
rs7874388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963774	0.91[JPT][hapmap]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4657	AUH	cis	cerebellum	SCAN
rs4657	NINJ1	cis	cerebellum	SCAN
rs4657	TDRD7	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:97839600-97850400	Strong transcription	HepG2	liver
8	chr9:97839600-97851000	Genic enhancers	A549	lung
9	chr9:97840000-97850000	Strong transcription	Osteobl	bone
10	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:97841200-97849800	Strong transcription	NH-A	brain
12	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:97841600-97849200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr9:97841600-97850000	Strong transcription	NHLF	lung
16	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
18	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:97842200-97849600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:97842200-97850600	Strong transcription	Fetal Lung	lung
22	chr9:97842200-97852000	Strong transcription	NHEK	skin
23	chr9:97842400-97850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:97842400-97850200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
26	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:97842800-97849400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:97842800-97849400	Strong transcription	NHDF-Ad	bronchial
29	chr9:97842800-97849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:97842800-97850800	Strong transcription	Placenta	Placenta
31	chr9:97843000-97849200	Strong transcription	Primary T cells from cord blood	blood
32	chr9:97843000-97850200	Strong transcription	Adipose Nuclei	Adipose
33	chr9:97843200-97849200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:97843200-97849400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:97843200-97851600	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr9:97843200-97851800	Genic enhancers	Brain Hippocampus Middle	brain
37	chr9:97843200-97852400	Genic enhancers	Rectal Smooth Muscle	rectum
38	chr9:97843400-97849800	Strong transcription	Hela-S3	cervix
39	chr9:97843600-97850200	Strong transcription	Ovary	ovary
40	chr9:97843600-97853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:97844000-97854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:97844400-97849600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:97844400-97852200	Strong transcription	Fetal Stomach	stomach
45	chr9:97844400-97854200	Weak transcription	Brain Germinal Matrix	brain
46	chr9:97845000-97852600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:97845200-97849400	Strong transcription	HMEC	breast
48	chr9:97845400-97850200	Weak transcription	Fetal Thymus	thymus
49	chr9:97845600-97849200	Strong transcription	Spleen	Spleen
50	chr9:97845600-97849600	Enhancers	Fetal Heart	heart

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