Variant report

Variant	rs9661993
Chromosome Location	chr1:153656405-153656406
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153651109..153660855-chr1:153698392..153702896,14	MCF-7	breast:
2	chr1:153649941..153652996-chr1:153654947..153657663,3	K562	blood:
3	chr1:153653996..153656594-chr1:153656905..153658985,2	MCF-7	breast:
4	chr1:153654218..153657204-chr1:153660557..153664055,3	MCF-7	breast:
5	chr1:153650729..153654060-chr1:153654100..153656603,4	MCF-7	breast:
6	chr1:153648584..153651991-chr1:153654471..153657777,3	MCF-7	breast:
7	chr1:153640859..153647825-chr1:153650423..153657512,10	K562	blood:
8	chr1:153640044..153642973-chr1:153654188..153656632,2	K562	blood:
9	chr1:153652339..153654108-chr1:153654445..153656447,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143621	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000169418	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1046381	0.87[EUR][1000 genomes]
rs10797056	0.85[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10797090	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10797096	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10908746	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908848	0.81[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11265625	0.85[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11265633	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1128894	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11580122	0.85[EUR][1000 genomes]
rs11588347	0.89[ASN][1000 genomes]
rs12564925	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1810836	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888115	0.85[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2274739	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2274740	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28379831	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28380060	0.85[CEU][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28510471	0.81[EUR][1000 genomes]
rs28580554	0.85[CEU][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28613361	0.82[EUR][1000 genomes]
rs28700217	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3790411	0.88[JPT][hapmap]
rs3790412	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3795396	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806234	0.85[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3818632	0.85[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3828031	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3862047	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4351684	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4515830	0.90[CHB][hapmap]
rs4845557	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845563	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs4845564	0.87[ASN][1000 genomes]
rs55772653	0.90[ASN][1000 genomes]
rs61806722	0.84[EUR][1000 genomes]
rs6427640	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674929	0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7345	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7934	0.85[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs913860	0.85[CEU][hapmap];0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs913861	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9662664	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer 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	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9661993	S100A13	cis	Lymphoblastoid	GTEx
rs9661993	S100A13	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153652400-153664600	Weak transcription	Gastric	stomach
2	chr1:153652400-153669800	Weak transcription	Pancreas	Pancrea
3	chr1:153653000-153669800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:153653200-153664000	Weak transcription	Left Ventricle	heart
5	chr1:153653200-153669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153653400-153663200	Strong transcription	Ovary	ovary
7	chr1:153653600-153656800	Genic enhancers	Adipose Nuclei	Adipose
8	chr1:153653600-153659600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:153653800-153666400	Strong transcription	Lung	lung
10	chr1:153653800-153669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:153654400-153657400	Weak transcription	Right Atrium	heart
12	chr1:153654400-153669200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:153654400-153669400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:153654800-153659400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:153655400-153656600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:153655400-153658000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:153655400-153660800	Weak transcription	Spleen	Spleen
18	chr1:153655400-153669800	Weak transcription	Esophagus	oesophagus
19	chr1:153655800-153657800	Strong transcription	Right Ventricle	heart
20	chr1:153656000-153656600	Genic enhancers	Fetal Kidney	kidney
21	chr1:153656000-153656800	Genic enhancers	Aorta	Aorta
22	chr1:153656000-153657400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:153656000-153657400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:153656200-153656800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:153656200-153659400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:153656400-153656600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:153656400-153656600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:153656400-153656800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:153656400-153656800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:153656400-153656800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:153656400-153656800	Enhancers	A549	lung
32	chr1:153656400-153656800	Enhancers	Hela-S3	cervix
33	chr1:153656400-153656800	Bivalent Enhancer	NHLF	lung
34	chr1:153656400-153657400	Enhancers	Stomach Mucosa	stomach
35	chr1:153656400-153659600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:153656400-153659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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