Variant report

Variant	rs12693524
Chromosome Location	chr2:189834437-189834438
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	MAFK	chr2:189834429-189834763	HepG2	liver:	n/a	chr2:189834677-189834692
2	GATA3	chr2:189833843-189834571	SK-N-SH	brain:	n/a	chr2:189834085-189834096
3	JUND	chr2:189833806-189834479	SK-N-SH	brain:	n/a	chr2:189834164-189834174 chr2:189834165-189834172 chr2:189834303-189834313 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834163-189834175 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834164-189834174
4	CEBPB	chr2:189834071-189834731	IMR90	lung:	n/a	n/a
5	EP300	chr2:189833896-189834476	SK-N-SH	brain:	n/a	chr2:189834165-189834174
6	JUND	chr2:189833844-189834556	SK-N-SH	brain:	n/a	chr2:189834164-189834174 chr2:189834165-189834172 chr2:189834303-189834313 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834163-189834175 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834164-189834174
7	MAFK	chr2:189834176-189834768	IMR90	lung:	n/a	chr2:189834677-189834692
8	TCF12	chr2:189833758-189834506	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr2:189833760-189834454	A549	lung:	n/a	n/a
10	EP300	chr2:189833786-189834628	SK-N-SH	brain:	n/a	chr2:189834165-189834174
11	PBX3	chr2:189833919-189834537	SK-N-SH	brain:	n/a	n/a
12	JUND	chr2:189833766-189834563	SK-N-SH	brain:	n/a	chr2:189834164-189834174 chr2:189834165-189834172 chr2:189834303-189834313 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834163-189834175 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834164-189834174
13	TCF12	chr2:189833820-189834601	SK-N-SH	brain:	n/a	n/a
14	FOSL2	chr2:189833898-189834531	SK-N-SH	brain:	n/a	chr2:189834164-189834174 chr2:189834165-189834172 chr2:189834303-189834313 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834163-189834175 chr2:189834164-189834174 chr2:189834165-189834173 chr2:189834164-189834174
15	GATA3	chr2:189833680-189834659	SK-N-SH	brain:	n/a	chr2:189834085-189834096

Variant related genes	Relation type
COL3A1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10208496	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1040186	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618257	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693519	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12693520	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12693522	0.88[ASN][1000 genomes]
rs12693523	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12990937	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13023280	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1516443	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1878199	1.00[ASN][1000 genomes]
rs1878200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138533	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2351418	0.88[ASN][1000 genomes]
rs4667254	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434304	0.87[ASN][1000 genomes]
rs6434305	1.00[ASN][1000 genomes]
rs7426072	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7603905	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv875608	chr2:189753823-189837995	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849974	chr2:189796272-189837995	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584056	chr2:189796272-189841052	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875611	chr2:189799499-189837212	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
11	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189828400-189838400	Weak transcription	Fetal Kidney	kidney
2	chr2:189830800-189839000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:189831200-189834800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:189831800-189836000	Weak transcription	Ovary	ovary
5	chr2:189832000-189834800	Weak transcription	HSMM	muscle
6	chr2:189832600-189836400	Enhancers	Colon Smooth Muscle	Colon
7	chr2:189833600-189834600	Enhancers	Fetal Stomach	stomach
8	chr2:189833600-189835200	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:189833600-189836400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:189833600-189836400	Enhancers	HSMMtube	muscle
11	chr2:189833600-189836600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:189833600-189836600	Enhancers	Osteobl	bone
13	chr2:189833600-189836800	Enhancers	Fetal Lung	lung
14	chr2:189834000-189835600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:189834200-189834600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:189834200-189834600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:189834200-189835000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:189834200-189838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:189834200-189838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:189834200-189842800	Weak transcription	A549	lung
21	chr2:189834400-189834800	Active TSS	Adipose Nuclei	Adipose
22	chr2:189834400-189834800	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:189834400-189835200	Flanking Active TSS	NHDF-Ad	bronchial
24	chr2:189834400-189836400	Enhancers	NHLF	lung
25	chr2:189834400-189838200	Weak transcription	Fetal Muscle Leg	muscle

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