Variant report

Variant	rs12890430
Chromosome Location	chr14:104293534-104293535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104292577..104296739-chr14:104312700..104315597,4	MCF-7	breast:
2	chr14:104292519..104294178-chr14:104297245..104300059,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258735	Chromatin interaction
ENSG00000088808	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10129899	0.86[ASN][1000 genomes]
rs1187417	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588797	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12879529	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12883337	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12885509	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12886637	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12888002	0.82[EUR][1000 genomes]
rs12890354	0.82[EUR][1000 genomes]
rs12890822	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890837	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12891477	0.88[ASN][1000 genomes]
rs12892189	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12893623	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17791722	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34596177	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35085624	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35740217	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861678	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4900597	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906363	0.82[EUR][1000 genomes]
rs4906364	0.81[AMR][1000 genomes]
rs4906376	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906377	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906378	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4906379	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6576006	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6576007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6576008	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66676135	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66953418	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7142769	0.80[EUR][1000 genomes]
rs722637	0.86[EUR][1000 genomes]
rs8017200	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9888591	0.87[AMR][1000 genomes];0.89[EUR][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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
9	nsv902320	chr14:104274294-104308095	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1838047	chr14:104283104-104359121	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12890430	XRCC3	cis	Whole Blood	GTEx
rs12890430	RP11-73M18.8	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104280800-104294800	Weak transcription	Small Intestine	intestine
2	chr14:104286200-104294800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:104286600-104294800	Weak transcription	Brain Angular Gyrus	brain
4	chr14:104286600-104303400	Weak transcription	Spleen	Spleen
5	chr14:104287000-104294800	Weak transcription	Adipose Nuclei	Adipose
6	chr14:104287200-104294800	Weak transcription	Ovary	ovary
7	chr14:104287200-104294800	Weak transcription	Right Ventricle	heart
8	chr14:104287600-104294800	Weak transcription	Fetal Lung	lung
9	chr14:104290000-104294400	Weak transcription	Right Atrium	heart
10	chr14:104291800-104294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:104292000-104294800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:104292000-104294800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr14:104292000-104312400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr14:104292200-104294800	Weak transcription	Fetal Kidney	kidney
15	chr14:104292200-104303800	Weak transcription	HepG2	liver
16	chr14:104292800-104294200	Weak transcription	Fetal Heart	heart
17	chr14:104292800-104294400	Weak transcription	Left Ventricle	heart
18	chr14:104292800-104294800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr14:104292800-104294800	Weak transcription	Pancreas	Pancrea
20	chr14:104292800-104294800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr14:104292800-104294800	Weak transcription	Stomach Mucosa	stomach
22	chr14:104292800-104298600	Weak transcription	A549	lung
23	chr14:104292800-104309000	Weak transcription	Fetal Intestine Small	intestine
24	chr14:104293000-104294800	Weak transcription	Liver	Liver
25	chr14:104293000-104295000	Weak transcription	Fetal Intestine Large	intestine

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