Variant report

Variant	rs13373831
Chromosome Location	chr1:228193791-228193792
allele	A/G
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	GABPA	chr1:228193790-228194503	H1-hESC	embryonic stem cell:	n/a	chr1:228194338-228194347
2	SUZ12	chr1:228193119-228194429	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr1:228191942-228194483	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr1:228193664-228194085	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228192133..228194243-chr1:228287809..228289393,2	K562	blood:
2	chr1:228184192..228186220-chr1:228191479..228194171,2	MCF-7	breast:
3	chr1:228193720..228196616-chr1:228296879..228298469,2	MCF-7	breast:
4	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:

Variant related genes	Relation type
WNT3A	TF binding region
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1155358	0.84[ASN][1000 genomes]
rs1323023	0.93[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.85[MKK][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3121309	0.82[MKK][hapmap]
rs4066662	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56772497	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58978756	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60356098	0.83[ASN][1000 genomes]
rs60408515	0.86[ASN][1000 genomes]
rs6426490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675355	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701785	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs708124	0.82[MKK][hapmap]
rs7515849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516358	1.00[AMR][1000 genomes]
rs7517798	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7529664	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[ASN][1000 genomes]
rs7541491	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.88[ASN][1000 genomes]
rs875980	0.86[AMR][1000 genomes]
rs881398	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription 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	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv826953	chr1:228191929-228196867	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3345664	chr1:228193354-228196202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3391367	chr1:228193679-228195777	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228191000-228194400	Weak transcription	Right Atrium	heart
2	chr1:228191800-228193800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr1:228191800-228194000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:228191800-228194200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:228192000-228194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:228192000-228194600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:228192000-228194600	Bivalent Enhancer	Fetal Stomach	stomach
8	chr1:228192200-228194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:228192200-228196800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:228192400-228193800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
11	chr1:228192400-228195200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr1:228192600-228194200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:228192600-228194400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:228192800-228194800	Bivalent Enhancer	Placenta	Placenta
15	chr1:228193200-228194200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr1:228193200-228194200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
17	chr1:228193400-228193800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
18	chr1:228193400-228193800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr1:228193400-228194000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:228193400-228194200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr1:228193400-228194400	Bivalent Enhancer	Esophagus	oesophagus
22	chr1:228193400-228196600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:228193600-228193800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr1:228193600-228193800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr1:228193600-228193800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:228193600-228194000	Bivalent Enhancer	NHEK	skin
27	chr1:228193600-228194400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:228193600-228195000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:228193600-228196200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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