Variant report

Variant	rs74089562
Chromosome Location	chr12:49937392-49937393
allele	A/T
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	MYBL2	chr12:49937068-49937413	HepG2	liver:	n/a	n/a
2	MAX	chr12:49936968-49937705	HepG2	liver:	n/a	chr12:49937364-49937377 chr12:49937365-49937376 chr12:49937366-49937376 chr12:49937369-49937377
3	EP300	chr12:49937375-49937416	HepG2	liver:	n/a	n/a
4	MYC	chr12:49937273-49937464	HepG2	liver:	n/a	chr12:49937364-49937377 chr12:49937365-49937376 chr12:49937366-49937376 chr12:49937369-49937377
5	MAX	chr12:49937194-49937394	HepG2	liver:	n/a	chr12:49937364-49937377 chr12:49937365-49937376 chr12:49937366-49937376 chr12:49937369-49937377
6	HNF4A	chr12:49937192-49937467	HepG2	liver:	n/a	chr12:49937307-49937319 chr12:49937305-49937320 chr12:49937305-49937320 chr12:49937302-49937324 chr12:49937306-49937319 chr12:49937305-49937320 chr12:49937307-49937319
7	MAX	chr12:49937210-49937495	K562	blood:	n/a	chr12:49937364-49937377 chr12:49937365-49937376 chr12:49937366-49937376 chr12:49937369-49937377
8	POLR2A	chr12:49937261-49937502	HepG2	liver:	n/a	n/a
9	HDAC2	chr12:49937027-49937396	HepG2	liver:	n/a	n/a
10	USF1	chr12:49937229-49937476	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49930852..49937653-chr12:49953841..49959391,7	K562	blood:
2	chr12:49937336..49938883-chr12:49959337..49961156,2	MCF-7	breast:
3	chr12:49936026..49937572-chr12:49942956..49945602,2	K562	blood:
4	chr12:49936941..49938508-chr12:49948825..49950668,2	MCF-7	breast:

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000187778	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11168999	1.00[ASN][1000 genomes]
rs11169023	1.00[ASN][1000 genomes]
rs12299908	1.00[ASN][1000 genomes]
rs12305457	1.00[ASN][1000 genomes]
rs12306194	1.00[ASN][1000 genomes]
rs12306785	1.00[ASN][1000 genomes]
rs12310836	1.00[ASN][1000 genomes]
rs12317050	1.00[ASN][1000 genomes]
rs12320273	1.00[ASN][1000 genomes]
rs12322425	1.00[ASN][1000 genomes]
rs56014465	1.00[ASN][1000 genomes]
rs56140046	1.00[ASN][1000 genomes]
rs58095611	1.00[ASN][1000 genomes]
rs61733848	1.00[ASN][1000 genomes]
rs7132759	1.00[ASN][1000 genomes]
rs7299820	1.00[ASN][1000 genomes]
rs7314265	1.00[ASN][1000 genomes]
rs73305039	1.00[ASN][1000 genomes]
rs73305072	1.00[ASN][1000 genomes]
rs73305076	1.00[ASN][1000 genomes]
rs73305095	1.00[ASN][1000 genomes]
rs7963130	1.00[ASN][1000 genomes]
rs7970334	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49933000-49942600	Weak transcription	Pancreas	Pancrea
2	chr12:49933400-49942000	Weak transcription	Right Ventricle	heart
3	chr12:49933400-49942400	Weak transcription	Right Atrium	heart
4	chr12:49933600-49937600	Weak transcription	Ovary	ovary
5	chr12:49934000-49937600	Weak transcription	Brain Anterior Caudate	brain
6	chr12:49934200-49942000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:49934600-49942200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:49935200-49937400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:49935200-49938200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:49935600-49937400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:49935800-49937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:49936200-49937600	Weak transcription	Esophagus	oesophagus
13	chr12:49936200-49939200	Bivalent Enhancer	Fetal Thymus	thymus
14	chr12:49936600-49938400	Enhancers	Spleen	Spleen
15	chr12:49936800-49937400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr12:49936800-49937600	Flanking Active TSS	HepG2	liver
17	chr12:49936800-49938200	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr12:49937000-49937800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:49937000-49938000	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr12:49937200-49937400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:49937200-49937400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:49937200-49937400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:49937200-49938400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr12:49937200-49939000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links