Variant report

Variant	rs2802273
Chromosome Location	chr1:227175802-227175803
allele	C/T
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:8)
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	SIN3AK20	chr1:227175679-227176395	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:227175801-227176333	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:227171755-227176557	K562	blood:	n/a	n/a
4	POLR2A	chr1:227174808-227176568	HL-60	blood:	n/a	n/a
5	POLR2A	chr1:227170173-227176506	K562	blood:	n/a	n/a
6	FOSL2	chr1:227175253-227176471	HepG2	liver:	n/a	chr1:227176439-227176451
7	RAD21	chr1:227175765-227176327	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:227174968-227176363	HL-60	blood:	n/a	n/a
9	FOXA1	chr1:227175791-227176191	HepG2	liver:	n/a	chr1:227176037-227176052
10	POLR2A	chr1:227169948-227179599	K562	blood:	n/a	n/a
11	HDAC2	chr1:227175793-227176305	MCF-7	breast:	n/a	chr1:227175926-227175945 chr1:227176039-227176048 chr1:227175807-227175821
12	CCNT2	chr1:227175775-227175975	K562	blood:	n/a	n/a
13	POLR2A	chr1:227170107-227176585	K562	blood:	n/a	n/a
14	ELF1	chr1:227175769-227176386	MCF-7	breast:	n/a	n/a
15	POLR2A	chr1:227174148-227176843	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227166708..227168288-chr1:227175078..227176909,2	MCF-7	breast:
2	chr1:227165601..227167978-chr1:227173311..227176266,3	MCF-7	breast:
3	chr1:227128683..227130385-chr1:227174300..227176049,2	MCF-7	breast:
4	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
5	chr1:227173983..227176329-chr1:227192052..227193578,2	MCF-7	breast:
6	chr1:227126152..227130822-chr1:227174735..227178540,5	MCF-7	breast:
7	chr1:227168074..227172579-chr1:227173053..227177156,6	MCF-7	breast:
8	chr1:227100125..227100781-chr1:227175209..227175979,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233706	TF binding region
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10482	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495261	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10495262	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10495264	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10495268	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10799385	0.85[AMR][1000 genomes]
rs10799386	0.87[AMR][1000 genomes]
rs10916091	0.87[AMR][1000 genomes]
rs10916094	0.87[AMR][1000 genomes]
rs10916096	0.83[AMR][1000 genomes]
rs11799444	0.81[ASN][1000 genomes]
rs11799547	0.81[ASN][1000 genomes]
rs11800145	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11800705	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11800897	0.81[ASN][1000 genomes]
rs11801093	0.81[ASN][1000 genomes]
rs11804358	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11808332	0.86[ASN][1000 genomes]
rs11808884	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11808903	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11810506	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11811176	0.81[ASN][1000 genomes]
rs11811824	0.80[ASN][1000 genomes]
rs12063170	0.87[AMR][1000 genomes]
rs12403161	0.85[ASN][1000 genomes]
rs12407082	0.81[ASN][1000 genomes]
rs12410431	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1289471	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1289472	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1289473	0.85[CEU][hapmap]
rs1320491	0.81[ASN][1000 genomes]
rs1320492	0.81[ASN][1000 genomes]
rs1343895	0.81[ASN][1000 genomes]
rs1343896	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1343897	0.81[ASN][1000 genomes]
rs1513623	0.87[AMR][1000 genomes]
rs16846833	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846836	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846842	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16846853	0.86[ASN][1000 genomes]
rs16846854	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846871	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16846890	0.81[ASN][1000 genomes]
rs16846892	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16846919	0.81[ASN][1000 genomes]
rs16846933	0.81[ASN][1000 genomes]
rs16846942	0.81[ASN][1000 genomes]
rs16846968	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16846989	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1757943	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1929853	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1929860	0.85[JPT][hapmap]
rs1929866	0.81[ASN][1000 genomes]
rs1929867	0.81[ASN][1000 genomes]
rs1929870	0.81[ASN][1000 genomes]
rs2225508	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2458520	0.81[ASN][1000 genomes]
rs2458522	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2482452	0.81[ASN][1000 genomes]
rs2492629	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2777835	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2802272	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2802274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2802276	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41268739	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653478	0.81[ASN][1000 genomes]
rs4653781	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653783	0.85[ASN][1000 genomes]
rs4653784	0.81[ASN][1000 genomes]
rs4653785	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653787	0.81[ASN][1000 genomes]
rs477162	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485674	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs489565	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs490517	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs497291	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs501772	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507967	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs511679	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs512538	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs529430	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs530057	0.81[ASN][1000 genomes]
rs531137	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs545171	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs555786	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556343	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs567677	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56781510	0.81[ASN][1000 genomes]
rs57244721	0.86[ASN][1000 genomes]
rs572561	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs583729	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs602585	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61133665	0.81[ASN][1000 genomes]
rs620991	0.81[ASN][1000 genomes]
rs621797	0.81[ASN][1000 genomes]
rs621874	0.81[ASN][1000 genomes]
rs629571	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426562	0.81[ASN][1000 genomes]
rs6426563	0.81[ASN][1000 genomes]
rs6426564	0.81[ASN][1000 genomes]
rs6426565	0.81[ASN][1000 genomes]
rs6426567	0.82[EUR][1000 genomes]
rs6426568	0.87[AMR][1000 genomes]
rs647702	0.81[ASN][1000 genomes]
rs664617	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs664815	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6656723	0.87[AMR][1000 genomes]
rs666559	0.81[ASN][1000 genomes]
rs6672902	0.81[ASN][1000 genomes]
rs667621	0.81[ASN][1000 genomes]
rs6681424	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6702869	0.87[AMR][1000 genomes]
rs693735	0.81[ASN][1000 genomes]
rs73089754	0.81[ASN][1000 genomes]
rs73091767	0.81[ASN][1000 genomes]
rs73093498	0.81[ASN][1000 genomes]
rs7517177	0.87[AMR][1000 genomes]
rs7531576	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7537520	0.81[ASN][1000 genomes]
rs7538743	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7538778	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9426540	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9426545	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9426600	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9426601	0.81[ASN][1000 genomes]
rs9426602	0.81[ASN][1000 genomes]
rs9426603	0.81[ASN][1000 genomes]
rs9426606	0.90[CHB][hapmap];1.00[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS 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	18 gene(s)	inside rSNPs	diseases
4	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
4	chr1:227154800-227176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227160000-227177200	Weak transcription	GM12878-XiMat	blood
7	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227162200-227176000	Strong transcription	Primary T cells from cord blood	blood
9	chr1:227162400-227181600	Weak transcription	NHEK	skin
10	chr1:227162600-227176600	Strong transcription	Thymus	Thymus
11	chr1:227163000-227180000	Weak transcription	HSMM	muscle
12	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:227163800-227176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
15	chr1:227165000-227176000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:227170000-227176000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:227170400-227176200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:227170400-227176400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:227170400-227177600	Strong transcription	Fetal Brain Female	brain
20	chr1:227170600-227177600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:227170800-227176200	Genic enhancers	Left Ventricle	heart
22	chr1:227172600-227177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:227172800-227176200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:227172800-227176200	Genic enhancers	Spleen	Spleen
25	chr1:227172800-227176600	Weak transcription	HSMMtube	muscle
26	chr1:227173000-227176000	Strong transcription	Fetal Stomach	stomach
27	chr1:227173200-227177400	Enhancers	Brain Angular Gyrus	brain
28	chr1:227173200-227178200	Weak transcription	Fetal Kidney	kidney
29	chr1:227173400-227176000	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr1:227173400-227176600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:227173400-227178200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:227173400-227178600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:227173600-227176000	Strong transcription	NHLF	lung
35	chr1:227173800-227176600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:227173800-227177200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:227173800-227177600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:227173800-227178400	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:227174000-227176400	Strong transcription	Osteobl	bone
40	chr1:227174000-227178200	Enhancers	Brain Substantia Nigra	brain
41	chr1:227174200-227176000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:227174200-227176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:227174200-227176200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:227174200-227176400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:227174400-227176400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:227174600-227176200	Genic enhancers	Brain Anterior Caudate	brain
47	chr1:227174600-227176200	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:227174800-227176600	Strong transcription	HUVEC	blood vessel
49	chr1:227174800-227176800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:227174800-227176800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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