Variant report

Variant	rs1056875
Chromosome Location	chr12:49580180-49580181
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	POLR2A	chr12:49580021-49580666	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:49579996-49580684	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:49579939-49583650	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:49580045-49580640	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:49580068-49580261	ProgFib	skin:	n/a	n/a
6	POLR2A	chr12:49579954-49580658	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:49579969-49580652	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:49580039-49580640	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:49580010-49580840	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:49579955-49580663	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:49579936-49580517	H1-neurons	neurons:	n/a	n/a
12	REST	chr12:49579315-49585380	H1-neurons	neurons:	n/a	chr12:49581154-49581167 chr12:49581154-49581167 chr12:49581714-49581734 chr12:49582472-49582485 chr12:49581151-49581171 chr12:49580352-49580362 chr12:49581151-49581171 chr12:49580345-49580358
13	POLR2A	chr12:49580047-49580782	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr12:49580043-49580666	GM12891	blood:	n/a	n/a
15	HEY1	chr12:49580028-49580660	K562	blood:	n/a	n/a
16	MXI1	chr12:49579985-49584758	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr12:49579948-49580706	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:49579957-49581448	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:49579958-49580692	GM12892	blood:	n/a	n/a
20	ZNF263	chr12:49580079-49580476	HEK293-T-REx	kidney:	n/a	chr12:49580281-49580302 chr12:49580258-49580279
21	POLR2A	chr12:49579965-49580444	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr12:49580112-49580505	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49523298..49526534-chr12:49578242..49583023,5	K562	blood:
2	chr12:49522685..49527255-chr12:49580115..49585539,18	MCF-7	breast:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10875927	0.81[EUR][1000 genomes]
rs10875928	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10875929	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875930	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875931	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11168884	0.80[EUR][1000 genomes]
rs11168890	0.80[EUR][1000 genomes]
rs11168894	0.80[EUR][1000 genomes]
rs11168901	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11168902	0.82[ASN][1000 genomes]
rs11168904	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11168909	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12227770	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229524	0.82[EUR][1000 genomes]
rs12579015	0.81[EUR][1000 genomes]
rs1874908	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1991427	0.81[EUR][1000 genomes]
rs1991428	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2114845	0.81[EUR][1000 genomes]
rs2162643	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2334930	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2334931	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2878287	0.80[EUR][1000 genomes]
rs58336603	0.81[EUR][1000 genomes]
rs6580701	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6580703	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs697624	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311346	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7953169	0.85[EUR][1000 genomes]
rs7954521	0.80[EUR][1000 genomes]
rs7954530	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7957998	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9739878	0.85[EUR][1000 genomes]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv976610	chr12:49577937-49580571	Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49570600-49581000	Weak transcription	GM12878-XiMat	blood
2	chr12:49574200-49580600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:49576000-49580800	Weak transcription	A549	lung
4	chr12:49576200-49580800	Weak transcription	Fetal Kidney	kidney
5	chr12:49576800-49581800	Weak transcription	Liver	Liver
6	chr12:49577000-49580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:49577000-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:49577200-49580200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:49577200-49580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:49577200-49581000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:49577200-49581000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:49577400-49580200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:49577400-49580200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:49577400-49580400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:49577400-49580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:49577400-49580800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:49577400-49581000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:49577400-49581000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:49577400-49581000	Weak transcription	Colonic Mucosa	Colon
20	chr12:49577400-49581000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:49577400-49581800	Weak transcription	Pancreas	Pancrea
22	chr12:49577400-49581800	Weak transcription	Small Intestine	intestine
23	chr12:49577600-49580600	Strong transcription	Adipose Nuclei	Adipose
24	chr12:49577600-49580800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:49577600-49581000	Strong transcription	Primary T cells from cord blood	blood
26	chr12:49577600-49581000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
27	chr12:49577800-49580200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:49577800-49580200	Strong transcription	Lung	lung
29	chr12:49577800-49580200	Weak transcription	HMEC	breast
30	chr12:49577800-49580200	Strong transcription	Osteobl	bone
31	chr12:49577800-49580400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:49577800-49580400	Strong transcription	Left Ventricle	heart
33	chr12:49577800-49580800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:49577800-49580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:49577800-49581000	Strong transcription	Thymus	Thymus
36	chr12:49577800-49581800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:49578000-49580200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:49578000-49580400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:49578000-49581000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:49578000-49581200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:49578000-49581400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49578200-49580400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:49578200-49580400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:49578200-49580600	Strong transcription	Spleen	Spleen
45	chr12:49578200-49580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:49578200-49580800	Strong transcription	Fetal Lung	lung
47	chr12:49578200-49580800	Strong transcription	Fetal Thymus	thymus
48	chr12:49578200-49581000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:49578200-49581000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:49578200-49581000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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