Variant report

Variant	rs73092957
Chromosome Location	chr1:228284371-228284372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228283602-228288407	K562	blood:	n/a	n/a
3	POLR2A	chr1:228284250-228284429	A549	lung:	n/a	n/a
4	POLR2A	chr1:228282889-228288572	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:228283138-228288342	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:228284041-228285838	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:228284138-228294734	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:228283629-228284474	U87	brain:	n/a	n/a
9	POLR2A	chr1:228283824-228288153	K562	blood:	n/a	n/a
10	POLR2A	chr1:228282920-228289800	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:228283571-228285986	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:228283284-228284619	K562	blood:	n/a	n/a
13	POLR2A	chr1:228283300-228288960	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:228283783-228289635	K562	blood:	n/a	n/a
15	POLR2A	chr1:228283072-228285818	GM19193	blood:	n/a	n/a
16	POLR2A	chr1:228284089-228284574	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:228284337-228284426	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:228283248-228289096	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:228283911-228284441	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:228284251-228284428	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:228283873-228285780	A549	lung:	n/a	n/a
23	POLR2A	chr1:228283647-228285922	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:228284245-228284395	A549	lung:	n/a	n/a
25	POLR2A	chr1:228282873-228290384	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:228283726-228293977	K562	blood:	n/a	n/a
27	POLR2A	chr1:228283870-228284911	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:228284256-228284440	A549	lung:	n/a	n/a
29	POLR2A	chr1:228283134-228289712	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:228284035-228286763	HL-60	blood:	n/a	n/a
31	POLR2A	chr1:228284111-228284567	A549	lung:	n/a	n/a
32	POLR2A	chr1:228284261-228284562	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:228283846-228290152	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr1:228284213-228284634	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr1:228283994-228285856	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr1:228284018-228285633	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:228284289-228284446	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:228284115-228284999	MCF-7	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228283995..228287162-chr1:228352238..228356052,3	K562	blood:
2	chr1:228282033..228284613-chr1:228342310..228344410,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2231715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2231720	1.00[AMR][1000 genomes]
rs56756911	1.00[AMR][1000 genomes]
rs56832724	1.00[AMR][1000 genomes]
rs56986798	1.00[AMR][1000 genomes]
rs57053910	1.00[AMR][1000 genomes]
rs57114383	1.00[AFR][1000 genomes]
rs59699324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61413658	1.00[AMR][1000 genomes]
rs6694537	1.00[AMR][1000 genomes]
rs6704401	1.00[AMR][1000 genomes]
rs73092912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092923	1.00[AMR][1000 genomes]
rs73092944	1.00[AMR][1000 genomes]
rs73092953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092954	1.00[AMR][1000 genomes]
rs73092959	1.00[AMR][1000 genomes]
rs73092999	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73095404	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73095424	1.00[AMR][1000 genomes]
rs73095429	1.00[AMR][1000 genomes]
rs73095437	1.00[AMR][1000 genomes]
rs73095449	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
8	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
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
4	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
9	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
10	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:228279600-228285600	Weak transcription	NH-A	brain
12	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
14	chr1:228280200-228284400	ZNF genes & repeats	Fetal Brain Female	brain
15	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
16	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
18	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
19	chr1:228281400-228289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:228282400-228284600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:228282400-228289200	Strong transcription	NHEK	skin
22	chr1:228282600-228284600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:228282600-228285000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:228282600-228285200	Weak transcription	HMEC	breast
25	chr1:228282600-228285600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:228282600-228286400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:228282600-228287200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:228282600-228288800	Strong transcription	K562	blood
29	chr1:228282600-228289000	Strong transcription	Primary T cells from cord blood	blood
30	chr1:228282800-228284400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:228282800-228284600	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr1:228282800-228284600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:228282800-228285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:228282800-228285200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:228282800-228285200	Weak transcription	HUVEC	blood vessel
36	chr1:228282800-228287400	Strong transcription	GM12878-XiMat	blood
37	chr1:228282800-228287800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:228282800-228288000	Strong transcription	Brain Substantia Nigra	brain
39	chr1:228282800-228289000	Strong transcription	Fetal Lung	lung
40	chr1:228282800-228289200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:228282800-228289200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:228283000-228284400	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr1:228283000-228284600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:228283000-228285000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:228283000-228285200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:228283000-228288800	Strong transcription	Dnd41	blood
47	chr1:228283000-228289000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:228283000-228289000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:228283000-228289200	Strong transcription	Brain Anterior Caudate	brain
50	chr1:228283200-228284400	Enhancers	Left Ventricle	heart

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