Variant report

Variant	rs74089557
Chromosome Location	chr12:49930366-49930367
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	ZNF263	chr12:49929919-49930861	HEK293-T-REx	kidney:	n/a	chr12:49930422-49930443
2	POLR2A	chr12:49930143-49930432	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:49930043-49930385	HUVEC	blood vessel:	n/a	n/a
4	NFIC	chr12:49929816-49930456	ECC-1	luminal epithelium:	n/a	chr12:49930178-49930206
5	SPI1	chr12:49930297-49930847	HL-60	blood:	n/a	n/a
6	POLR2A	chr12:49929702-49930417	A549	lung:	n/a	n/a
7	POLR2A	chr12:49929416-49930427	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:49930331-49930423	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49668500..49671128-chr12:49928861..49931681,2	MCF-7	breast:
2	chr12:49759022..49764027-chr12:49928293..49932911,8	MCF-7	breast:
3	chr12:49759326..49761606-chr12:49928836..49931818,3	MCF-7	breast:
4	chr12:49925851..49930721-chr12:49933231..49936704,4	MCF-7	breast:

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1012874	0.86[ASN][1000 genomes]
rs10506287	0.86[ASN][1000 genomes]
rs10506288	0.86[ASN][1000 genomes]
rs11169126	0.86[ASN][1000 genomes]
rs11169143	0.86[ASN][1000 genomes]
rs11169145	0.86[ASN][1000 genomes]
rs11830696	0.86[ASN][1000 genomes]
rs11836837	0.86[ASN][1000 genomes]
rs11837639	0.86[ASN][1000 genomes]
rs12306422	0.86[ASN][1000 genomes]
rs12306430	0.86[ASN][1000 genomes]
rs12306481	0.86[ASN][1000 genomes]
rs12307828	0.86[ASN][1000 genomes]
rs12313354	0.86[ASN][1000 genomes]
rs12315524	0.86[ASN][1000 genomes]
rs12317778	0.86[ASN][1000 genomes]
rs1317131	0.86[ASN][1000 genomes]
rs17123764	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17123927	0.86[ASN][1000 genomes]
rs17123970	0.86[ASN][1000 genomes]
rs1993398	0.86[ASN][1000 genomes]
rs2336447	0.86[ASN][1000 genomes]
rs4641552	0.86[ASN][1000 genomes]
rs55637397	0.86[ASN][1000 genomes]
rs56737983	0.86[ASN][1000 genomes]
rs56743994	0.86[ASN][1000 genomes]
rs56906356	0.86[ASN][1000 genomes]
rs56945609	0.86[ASN][1000 genomes]
rs57291131	0.86[ASN][1000 genomes]
rs57398316	0.81[AFR][1000 genomes]
rs58756176	0.86[ASN][1000 genomes]
rs59261129	0.86[ASN][1000 genomes]
rs60094911	0.86[ASN][1000 genomes]
rs60126713	0.86[ASN][1000 genomes]
rs60415769	0.86[ASN][1000 genomes]
rs60613973	0.86[ASN][1000 genomes]
rs61281663	0.86[ASN][1000 genomes]
rs7298080	0.86[ASN][1000 genomes]
rs74086911	0.86[ASN][1000 genomes]
rs74087113	0.86[ASN][1000 genomes]
rs74087134	0.86[ASN][1000 genomes]
rs74089551	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74089564	0.86[ASN][1000 genomes]
rs74089566	0.86[ASN][1000 genomes]
rs74089570	0.86[ASN][1000 genomes]
rs74089573	0.86[ASN][1000 genomes]
rs7487854	0.86[ASN][1000 genomes]
rs7953412	0.86[ASN][1000 genomes]
rs7964320	0.86[ASN][1000 genomes]
rs7968302	0.86[ASN][1000 genomes]
rs7970674	0.86[ASN][1000 genomes]
rs7971176	0.86[ASN][1000 genomes]
rs7971369	0.86[ASN][1000 genomes]
rs7973498	0.86[ASN][1000 genomes]
rs9805063	0.86[ASN][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	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49914400-49931400	Weak transcription	Pancreas	Pancrea
2	chr12:49916400-49931200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:49917600-49931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:49920000-49931200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:49920200-49931400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:49920600-49931200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:49920600-49931400	Weak transcription	Spleen	Spleen
8	chr12:49921800-49930800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:49921800-49931200	Weak transcription	Right Ventricle	heart
10	chr12:49922000-49931200	Weak transcription	HSMMtube	muscle
11	chr12:49927400-49931200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:49928800-49931200	Enhancers	Primary B cells from cord blood	blood
13	chr12:49929600-49930400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:49929600-49930400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:49929600-49930400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
16	chr12:49929600-49930400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:49929600-49930400	Enhancers	NH-A	brain
18	chr12:49929600-49930600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:49929600-49931200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:49929600-49931400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:49929600-49931600	Enhancers	HMEC	breast
22	chr12:49929600-49931600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:49929800-49930400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr12:49929800-49930600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr12:49929800-49930600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:49929800-49930800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:49929800-49930800	Enhancers	Hela-S3	cervix
28	chr12:49929800-49931000	Enhancers	NHEK	skin
29	chr12:49929800-49931400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr12:49929800-49931400	Enhancers	A549	lung
31	chr12:49930000-49930400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr12:49930000-49930400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:49930000-49930400	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr12:49930000-49930400	Bivalent Enhancer	Fetal Kidney	kidney
35	chr12:49930000-49931200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:49930000-49931200	Enhancers	GM12878-XiMat	blood
37	chr12:49930200-49930400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr12:49930200-49930400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:49930200-49930400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:49930200-49930400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
41	chr12:49930200-49930400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
42	chr12:49930200-49930400	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr12:49930200-49930600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr12:49930200-49930800	Bivalent Enhancer	K562	blood
45	chr12:49930200-49931200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:49930200-49931400	Weak transcription	Esophagus	oesophagus

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