Variant report

Variant	rs66676135
Chromosome Location	chr14:104271504-104271505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104268190..104272252-chr14:104312561..104316180,5	MCF-7	breast:
2	chr14:104268895..104271672-chr14:104378681..104380449,2	MCF-7	breast:
3	chr14:104270610..104272155-chr14:104386224..104388963,2	MCF-7	breast:
4	chr14:104091792..104094435-chr14:104270981..104273053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088808	Chromatin interaction
ENSG00000156411	Chromatin interaction
ENSG00000258735	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10129899	0.85[ASN][1000 genomes]
rs1187417	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588797	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12879529	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12880821	0.81[ASN][1000 genomes]
rs12883337	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12885509	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886637	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12888002	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12890354	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12890430	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12890822	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890837	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12891477	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12892189	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12893623	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17791722	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2368560	0.81[ASN][1000 genomes]
rs34596177	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35085624	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35740217	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742366	0.85[AMR][1000 genomes]
rs3861678	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900597	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4906363	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906364	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4906376	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4906377	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4906378	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906379	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6576006	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6576007	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6576008	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66953418	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7142769	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7143885	0.81[AMR][1000 genomes]
rs722637	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8017200	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8548	0.83[AMR][1000 genomes]
rs9888591	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66676135	XRCC3	cis	Whole Blood	GTEx
rs66676135	RP11-73M18.8	cis	Artery Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104215400-104273200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr14:104218400-104277800	Weak transcription	Spleen	Spleen
3	chr14:104230600-104271600	Weak transcription	Esophagus	oesophagus
4	chr14:104236800-104272800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:104239000-104272400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr14:104241000-104274400	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:104257600-104272000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:104257800-104284000	Weak transcription	Gastric	stomach
9	chr14:104258800-104274800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr14:104262600-104277200	Weak transcription	Pancreas	Pancrea
11	chr14:104263000-104277400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:104263200-104281800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:104263600-104274600	Weak transcription	Liver	Liver
14	chr14:104263800-104275800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr14:104268600-104285600	Weak transcription	Lung	lung
16	chr14:104269200-104272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:104270200-104273800	Enhancers	Fetal Heart	heart
18	chr14:104270400-104272000	Enhancers	GM12878-XiMat	blood
19	chr14:104270600-104271600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr14:104270800-104271800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr14:104270800-104272200	Enhancers	Left Ventricle	heart
22	chr14:104270800-104272200	Weak transcription	Osteobl	bone
23	chr14:104271000-104273000	Weak transcription	Brain Angular Gyrus	brain
24	chr14:104271000-104285600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:104271200-104271800	Weak transcription	NHEK	skin
26	chr14:104271400-104271800	Enhancers	Right Ventricle	heart
27	chr14:104271400-104272800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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