Variant report

Variant	rs1169280
Chromosome Location	chr12:121455538-121455539
allele	C/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	ARID3A	chr12:121455416-121455815	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121447431..121451051-chr12:121452490..121455717,3	MCF-7	breast:
2	chr12:121454608..121456254-chr12:121460515..121463475,3	K562	blood:

Variant related genes	Relation type
C12orf43	TF binding region
ENSG00000157895	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10849828	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065393	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065403	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169304	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1169307	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12368199	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs12811390	0.87[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12819210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796419	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2257813	0.95[ASN][1000 genomes]
rs2258227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259697	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264779	0.95[ASN][1000 genomes]
rs2701180	0.97[ASN][1000 genomes]
rs2859394	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3999413	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4556628	1.00[JPT][hapmap];0.89[ASN][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121454400-121456400	Enhancers	K562	blood
2	chr12:121454400-121456800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:121454400-121458000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:121454400-121458200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:121454400-121458200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:121454400-121458400	Weak transcription	Spleen	Spleen
7	chr12:121454400-121461600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:121454400-121461800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:121454400-121462600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:121454400-121463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:121454400-121463200	Weak transcription	Small Intestine	intestine
12	chr12:121454400-121463600	Weak transcription	Lung	lung
13	chr12:121454400-121464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:121454400-121471600	Weak transcription	GM12878-XiMat	blood
15	chr12:121454400-121472200	Weak transcription	Primary T cells from cord blood	blood
16	chr12:121454400-121475800	Weak transcription	Adipose Nuclei	Adipose
17	chr12:121454400-121476000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:121454400-121476400	Weak transcription	Right Atrium	heart
19	chr12:121454600-121455800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:121454600-121456400	Enhancers	HepG2	liver
21	chr12:121454600-121457600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:121454600-121457600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:121454600-121457600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:121454600-121457800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:121454600-121458800	Weak transcription	Liver	Liver
26	chr12:121454600-121461400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:121454600-121462400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:121454600-121463400	Weak transcription	Hela-S3	cervix
29	chr12:121454600-121463800	Weak transcription	Colonic Mucosa	Colon
30	chr12:121454600-121470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:121454600-121471000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:121454600-121471000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:121454600-121471200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:121454600-121471600	Weak transcription	Fetal Thymus	thymus
35	chr12:121454600-121476200	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:121454600-121476200	Weak transcription	Gastric	stomach
37	chr12:121454800-121458800	Weak transcription	Stomach Mucosa	stomach
38	chr12:121454800-121461600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:121454800-121470400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:121454800-121471000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:121455400-121455600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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