Variant report

Variant	rs7048699
Chromosome Location	chr9:94708403-94708404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94667534..94670775-chr9:94707582..94710553,5	K562	blood:
2	chr9:94706737..94709425-chr9:94709648..94712474,2	MCF-7	breast:
3	chr9:94646595..94649139-chr9:94708273..94710120,2	K562	blood:
4	chr9:94706769..94709242-chr9:94710784..94712955,2	MCF-7	breast:
5	chr9:94533336..94534896-chr9:94707634..94709527,2	MCF-7	breast:
6	chr9:94708402..94710475-chr9:94715730..94717686,2	K562	blood:
7	chr9:94661900..94664292-chr9:94705248..94709269,4	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10116249	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118072	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10124760	0.95[EUR][1000 genomes]
rs10125384	0.86[EUR][1000 genomes]
rs10125466	0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10512220	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10733743	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739925	0.86[JPT][hapmap]
rs10761137	0.84[CEU][hapmap]
rs10761138	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10761143	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs10820931	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12340044	0.88[CEU][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1316268	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1609292	0.84[CEU][hapmap]
rs1881391	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1892268	0.84[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1919100	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2297568	0.83[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2312739	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2895201	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3847308	0.82[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479385	0.82[EUR][1000 genomes]
rs6479386	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6479387	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6479388	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479389	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479400	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479402	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7020136	0.84[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7023075	0.87[MEX][hapmap]
rs7034357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7034363	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7037255	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7038017	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7041193	0.83[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7042102	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7047326	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7848874	0.88[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7848987	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7850309	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7852032	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7859689	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7862779	0.86[EUR][1000 genomes]
rs7863167	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867072	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7869504	0.84[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7871444	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9774945	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv982625	chr9:94702344-94712887	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7048699	OMD	cis	cerebellum	SCAN
rs7048699	ZNF484	cis	cerebellum	SCAN
rs7048699	CDK20	cis	parietal	SCAN
rs7048699	C9orf170	cis	cerebellum	SCAN
rs7048699	ZNF484	cis	parietal	SCAN
rs7048699	SPTLC1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94706200-94710400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr9:94706400-94708800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:94706800-94709600	Flanking Active TSS	K562	blood
4	chr9:94707000-94708800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:94707000-94708800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:94707000-94709800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:94707200-94708800	Enhancers	Placenta	Placenta
8	chr9:94707400-94708600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:94707400-94708800	Enhancers	Colonic Mucosa	Colon
10	chr9:94707400-94710400	Weak transcription	Gastric	stomach
11	chr9:94707600-94708600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:94707600-94708600	Flanking Active TSS	Fetal Lung	lung
13	chr9:94707600-94708600	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr9:94707600-94708800	Flanking Active TSS	Hela-S3	cervix
15	chr9:94707600-94709000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:94707600-94709400	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr9:94707600-94709600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:94707600-94709800	Enhancers	Fetal Intestine Small	intestine
19	chr9:94707600-94710400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr9:94707800-94708600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr9:94707800-94709200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:94708000-94709000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr9:94708000-94709200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:94708000-94709400	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr9:94708200-94708600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:94708200-94708600	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr9:94708200-94708600	Flanking Active TSS	Fetal Stomach	stomach
28	chr9:94708200-94708800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:94708200-94709000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr9:94708200-94709200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:94708200-94709200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:94708200-94709600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr9:94708200-94710400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:94708400-94708600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr9:94708400-94708600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:94708400-94708600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:94708400-94708600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:94708400-94708600	Bivalent/Poised TSS	Fetal Brain Male	brain
39	chr9:94708400-94708800	Active TSS	Fetal Kidney	kidney
40	chr9:94708400-94708800	Enhancers	NHLF	lung
41	chr9:94708400-94709000	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr9:94708400-94709200	Enhancers	Ovary	ovary
43	chr9:94708400-94709200	Enhancers	Right Atrium	heart
44	chr9:94708400-94709200	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr9:94708400-94709400	Enhancers	Fetal Heart	heart
46	chr9:94708400-94710000	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr9:94708400-94710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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