Variant report

Variant	rs4974480
Chromosome Location	chr3:134178562-134178563
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134177048..134179996-chr3:134183528..134186034,2	MCF-7	breast:
2	chr3:134090280..134093272-chr3:134177192..134180095,2	MCF-7	breast:
3	chr3:134077067..134080470-chr3:134177227..134178995,3	MCF-7	breast:
4	chr3:134147507..134149518-chr3:134176090..134178859,2	MCF-7	breast:
5	chr3:134170227..134173961-chr3:134177457..134180784,3	MCF-7	breast:
6	chr3:134177467..134180385-chr3:134192923..134195791,2	MCF-7	breast:
7	chr3:134177254..134179184-chr3:134182489..134185436,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 208 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:204)

rs_ID	r²[population]
rs10935113	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935120	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs1138273	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11706117	0.90[EUR][1000 genomes]
rs11708531	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11915964	0.91[CEU][hapmap]
rs11919350	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11927068	0.87[EUR][1000 genomes]
rs11928499	0.89[EUR][1000 genomes]
rs12490835	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs12492930	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12637301	0.88[CEU][hapmap]
rs12637751	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13059720	0.89[EUR][1000 genomes]
rs13064209	0.84[CEU][hapmap]
rs13065405	0.89[EUR][1000 genomes]
rs13065773	0.83[EUR][1000 genomes]
rs13075117	0.84[CEU][hapmap]
rs13075253	0.84[CEU][hapmap]
rs13076825	0.83[CEU][hapmap]
rs13081177	0.83[EUR][1000 genomes]
rs13081688	0.88[EUR][1000 genomes]
rs13084192	0.84[CEU][hapmap]
rs13087875	0.89[EUR][1000 genomes]
rs13089566	0.88[CEU][hapmap]
rs13089966	0.83[EUR][1000 genomes]
rs13096604	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs13098546	0.84[CEU][hapmap]
rs13316205	0.90[EUR][1000 genomes]
rs1357762	0.96[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs1357764	0.92[CEU][hapmap]
rs1498718	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1534025	0.96[CEU][hapmap]
rs1534026	0.83[EUR][1000 genomes]
rs1534027	0.83[EUR][1000 genomes]
rs1534028	0.83[EUR][1000 genomes]
rs1534030	0.83[CEU][hapmap]
rs17694011	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1814336	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1814337	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1863912	0.88[EUR][1000 genomes]
rs1863913	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1874883	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1880375	0.88[CEU][hapmap]
rs1880376	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1880377	0.87[EUR][1000 genomes]
rs1917130	0.91[CEU][hapmap]
rs2056603	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs2177601	0.89[EUR][1000 genomes]
rs2177602	0.89[EUR][1000 genomes]
rs2241556	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2293293	0.87[CEU][hapmap]
rs2293294	0.88[CEU][hapmap]
rs2370578	0.90[EUR][1000 genomes]
rs2370641	0.90[EUR][1000 genomes]
rs2370642	0.90[EUR][1000 genomes]
rs2373865	0.83[EUR][1000 genomes]
rs28409322	0.86[EUR][1000 genomes]
rs28702610	0.84[EUR][1000 genomes]
rs2887797	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2888670	0.87[CEU][hapmap]
rs35718987	0.83[EUR][1000 genomes]
rs35933983	0.86[EUR][1000 genomes]
rs36006513	0.83[EUR][1000 genomes]
rs3846055	0.90[EUR][1000 genomes]
rs3846056	0.90[EUR][1000 genomes]
rs3856729	0.90[EUR][1000 genomes]
rs3932818	0.95[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4074521	0.87[CEU][hapmap]
rs4074522	0.87[CEU][hapmap]
rs4245903	0.87[CEU][hapmap]
rs4245905	0.84[CEU][hapmap]
rs4245907	0.88[CEU][hapmap]
rs4306899	0.83[CEU][hapmap]
rs4309773	0.83[EUR][1000 genomes]
rs4367113	0.83[EUR][1000 genomes]
rs4417907	0.83[EUR][1000 genomes]
rs4435682	0.87[CEU][hapmap]
rs4437193	0.81[CEU][hapmap]
rs4456908	0.80[CEU][hapmap]
rs4498009	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4539979	0.96[CEU][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs4572812	0.81[EUR][1000 genomes]
rs4634170	0.83[CEU][hapmap]
rs4955468	0.80[CEU][hapmap]
rs4955525	0.87[CEU][hapmap]
rs4955526	0.87[CEU][hapmap]
rs4955534	0.88[CEU][hapmap]
rs4955542	0.87[CEU][hapmap]
rs4955546	0.82[CEU][hapmap]
rs4955547	0.83[CEU][hapmap]
rs4955555	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4974478	0.86[EUR][1000 genomes]
rs4974481	0.87[EUR][1000 genomes]
rs4974483	0.90[EUR][1000 genomes]
rs4974484	0.90[EUR][1000 genomes]
rs4974493	0.90[EUR][1000 genomes]
rs55913793	0.83[EUR][1000 genomes]
rs62269547	0.90[EUR][1000 genomes]
rs6439484	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6439487	0.89[EUR][1000 genomes]
rs6763088	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6763093	0.88[EUR][1000 genomes]
rs6763188	0.87[CEU][hapmap]
rs6764764	0.83[CEU][hapmap]
rs6765505	0.90[EUR][1000 genomes]
rs6766818	0.90[EUR][1000 genomes]
rs6766897	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6768323	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6769885	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6772406	0.90[EUR][1000 genomes]
rs6772896	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6775611	0.91[CEU][hapmap]
rs6776203	0.89[EUR][1000 genomes]
rs6779326	0.84[CEU][hapmap]
rs6782128	0.83[EUR][1000 genomes]
rs6785027	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6787371	0.89[EUR][1000 genomes]
rs6790338	0.90[EUR][1000 genomes]
rs6790466	0.89[EUR][1000 genomes]
rs6799110	0.90[EUR][1000 genomes]
rs6799543	0.89[EUR][1000 genomes]
rs6800862	0.95[CEU][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs6801596	0.87[EUR][1000 genomes]
rs6802654	0.90[EUR][1000 genomes]
rs6804770	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6805388	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806417	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6806810	0.88[CEU][hapmap]
rs7356093	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7371896	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7373874	0.89[EUR][1000 genomes]
rs7374158	0.88[EUR][1000 genomes]
rs7374325	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7427492	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7428326	0.86[EUR][1000 genomes]
rs7429866	0.89[EUR][1000 genomes]
rs7430034	0.83[CEU][hapmap]
rs7432268	0.89[EUR][1000 genomes]
rs7433663	0.89[EUR][1000 genomes]
rs7611828	0.86[EUR][1000 genomes]
rs7619451	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7623567	0.91[CEU][hapmap]
rs7626557	0.92[CEU][hapmap]
rs7627726	0.86[EUR][1000 genomes]
rs7630874	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7637227	0.87[EUR][1000 genomes]
rs7648990	0.89[EUR][1000 genomes]
rs7649910	0.80[EUR][1000 genomes]
rs7653807	0.91[CEU][hapmap]
rs9289471	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9289475	0.89[EUR][1000 genomes]
rs9289476	0.96[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs9289478	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs934093	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs9809619	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9813774	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs9814567	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9815297	0.90[EUR][1000 genomes]
rs9815894	0.83[EUR][1000 genomes]
rs9815983	0.90[EUR][1000 genomes]
rs9819532	0.83[EUR][1000 genomes]
rs9820150	0.89[EUR][1000 genomes]
rs9820425	0.89[EUR][1000 genomes]
rs9824185	0.88[CEU][hapmap]
rs9826496	0.90[EUR][1000 genomes]
rs9827672	0.85[EUR][1000 genomes]
rs9827987	0.83[EUR][1000 genomes]
rs9828815	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9829092	0.89[EUR][1000 genomes]
rs9832785	0.90[EUR][1000 genomes]
rs9833753	0.90[EUR][1000 genomes]
rs9834755	0.89[EUR][1000 genomes]
rs9835204	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9836401	0.84[CEU][hapmap]
rs9838119	0.84[CEU][hapmap]
rs9838467	0.84[CEU][hapmap]
rs9838834	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9841180	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9841212	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9841371	0.91[CEU][hapmap]
rs9844537	0.89[EUR][1000 genomes]
rs9847788	0.96[CEU][hapmap]
rs9848254	0.84[CEU][hapmap]
rs9850015	0.87[EUR][1000 genomes]
rs9851441	0.96[CEU][hapmap]
rs9854299	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs9855013	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9857242	0.87[CEU][hapmap]
rs9857995	0.87[CEU][hapmap]
rs9863786	0.88[EUR][1000 genomes]
rs9864346	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs9869981	0.88[EUR][1000 genomes]
rs9870262	0.88[EUR][1000 genomes]
rs9871226	0.84[CEU][hapmap]
rs9871305	0.90[EUR][1000 genomes]
rs9876658	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883753	0.95[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs9884031	0.89[EUR][1000 genomes]
rs9968172	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9985341	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9985356	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs9989967	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs9990351	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[EUR][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	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv877511	chr3:134174071-134358947	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv877512	chr3:134174071-134372486	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv877513	chr3:134174071-134379752	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs4974480	ANAPC13	cis	Heart Left Ventricle	GTEx
rs4974480	ANAPC13	cis	Esophagus Muscularis	GTEx
rs4974480	ANAPC13	cis	Nerve Tibial	GTEx
rs4974480	CEP63	cis	Muscle Skeletal	GTEx
rs4974480	ANAPC13	cis	Artery Tibial	GTEx
rs4974480	ANAPC13	cis	normal skin	skin_eQTL
rs4974480	CEP63	cis	Esophagus Mucosa	GTEx
rs4974480	ANAPC13	cis	lung	GTEx
rs4974480	ANAPC13	cis	Muscle Skeletal	GTEx
rs4974480	ANAPC13	cis	multi-tissue	Pritchard
rs4974480	CEP63	cis	Esophagus Muscularis	GTEx
rs4974480	ANAPC13	cis	lesional skin	skin_eQTL
rs4974480	ANAPC13	cis	uninvolved skin	skin_eQTL
rs4974480	CEP63	cis	lesional skin	skin_eQTL
rs4974480	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs4974480	ANAPC13	cis	Esophagus Mucosa	GTEx
rs4974480	ANAPC13	cis	Artery Aorta	GTEx
rs4974480	CEP63	cis	Nerve Tibial	GTEx
rs4974480	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs4974480	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs4974480	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs4974480	ANAPC13	cis	Thyroid	GTEx
rs4974480	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs4974480	CEP63	cis	Artery Tibial	GTEx
rs4974480	CEP63	cis	lung	GTEx
rs4974480	ANAPC13	cis	Stomach	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134166000-134181800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:134167200-134181800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:134169000-134183600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:134169200-134178600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:134169200-134180400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:134171000-134178600	Weak transcription	Osteobl	bone
7	chr3:134173000-134181200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:134173200-134180800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:134173200-134181000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:134175000-134180800	Weak transcription	Fetal Kidney	kidney
11	chr3:134176200-134178600	Enhancers	Pancreas	Pancrea
12	chr3:134176200-134182000	Weak transcription	Aorta	Aorta
13	chr3:134176600-134180000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:134176800-134180000	Weak transcription	NHEK	skin
15	chr3:134176800-134180800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:134176800-134180800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:134176800-134180800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:134176800-134182200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:134177000-134178600	Weak transcription	Adipose Nuclei	Adipose
20	chr3:134177000-134179400	Weak transcription	Right Atrium	heart
21	chr3:134177000-134179600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:134177000-134179600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:134177000-134181200	Weak transcription	Fetal Brain Male	brain
24	chr3:134177200-134179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:134177400-134181800	Weak transcription	Fetal Brain Female	brain
26	chr3:134177800-134180800	Weak transcription	Fetal Stomach	stomach
27	chr3:134178000-134180000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:134178000-134180800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:134178200-134181000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:134178200-134182600	Weak transcription	Fetal Intestine Small	intestine
31	chr3:134178400-134178600	Enhancers	Placenta	Placenta
32	chr3:134178400-134178600	Enhancers	Left Ventricle	heart
33	chr3:134178400-134178600	Enhancers	Right Ventricle	heart
34	chr3:134178400-134178800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:134178400-134179600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:134178400-134180200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:134178400-134180800	Enhancers	NHDF-Ad	bronchial
38	chr3:134178400-134182400	Enhancers	NHLF	lung
39	chr3:134178400-134186400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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