Variant report

Variant	rs6477998
Chromosome Location	chr9:115997249-115997250
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115995999..115998465-chr9:116001136..116003648,2	K562	blood:
2	chr9:115990891..115993253-chr9:115993931..115999009,4	K562	blood:
3	chr9:115991545..115993932-chr9:115995693..115997298,2	K562	blood:
4	chr9:115996965..115999527-chr9:116002148..116004164,2	K562	blood:
5	chr9:115982366..115985193-chr9:115997022..116000102,3	MCF-7	breast:
6	chr9:115995531..115997450-chr9:115998162..116001080,2	MCF-7	breast:
7	chr9:115988089..115990143-chr9:115997118..115999123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136868	Chromatin interaction
ENSG00000119321	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10123415	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125992	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513189	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739388	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739392	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759637	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759638	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10817461	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817468	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981715	0.87[CHB][hapmap]
rs11789755	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs11792628	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12343629	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2296073	0.82[CHB][hapmap]
rs3750532	0.86[CHB][hapmap]
rs3750533	0.87[CHB][hapmap]
rs3750534	0.87[CHB][hapmap]
rs4129395	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129396	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4284098	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4560868	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979231	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6477999	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7038769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859354	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9299214	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hematology traits	23303382	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6477998	SLC31A1	cis	Liver	GTEx
rs6477998	CDC26	cis	Esophagus Muscularis	GTEx
rs6477998	CDC26	cis	Adipose Subcutaneous	GTEx
rs6477998	SLC31A1	trans	multi-tissue	Pritchard
rs6477998	CDC26	cis	Muscle Skeletal	GTEx
rs6477998	ZNF618	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
2	chr9:115985200-115998000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:115985200-116001800	Weak transcription	Pancreas	Pancrea
4	chr9:115985600-115997600	Weak transcription	Brain Germinal Matrix	brain
5	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:115985800-116018400	Weak transcription	NHEK	skin
7	chr9:115985800-116019000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:115985800-116021000	Weak transcription	Fetal Stomach	stomach
9	chr9:115986400-116013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:115987600-115998600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:115987600-116017800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:115987600-116018200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:115987800-116011000	Weak transcription	A549	lung
14	chr9:115987800-116021000	Weak transcription	Hela-S3	cervix
15	chr9:115989000-116019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:115989200-116005600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:115991000-116011600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:115995200-116017800	Weak transcription	Left Ventricle	heart
19	chr9:115995400-116009200	Weak transcription	K562	blood
20	chr9:115995400-116018000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:115995800-115997800	Weak transcription	Small Intestine	intestine
22	chr9:115995800-115998600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr9:115995800-115999400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr9:115995800-116005200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:115996000-115998000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:115996000-115999200	Weak transcription	HepG2	liver
27	chr9:115996000-115999400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:115996000-116022200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:115996200-115997800	Weak transcription	NHLF	lung
31	chr9:115996200-115999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:115996200-116018600	Weak transcription	Primary T cells from cord blood	blood
33	chr9:115996200-116022400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:115996400-115997800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:115996400-115997800	Weak transcription	Adipose Nuclei	Adipose
36	chr9:115996400-115998000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:115996400-115998000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:115996400-115998400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr9:115996400-116000600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:115996400-116003200	Enhancers	Liver	Liver
41	chr9:115996600-115997800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:115996600-116019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:115996800-115997800	Enhancers	GM12878-XiMat	blood

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