Variant report

Variant	rs9841180
Chromosome Location	chr3:134191880-134191881
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134024950..134033700-chr3:134189216..134199294,13	MCF-7	breast:
2	chr3:134092717..134095501-chr3:134190720..134194395,3	MCF-7	breast:
3	chr3:134027019..134027846-chr3:134191593..134192140,2	K562	blood:
4	chr3:134191379..134193880-chr3:134203414..134206038,3	MCF-7	breast:
5	chr3:134188763..134190548-chr3:134191241..134193018,3	MCF-7	breast:
6	chr3:134087226..134089802-chr3:134191337..134194305,2	MCF-7	breast:
7	chr3:134075315..134078566-chr3:134189782..134194003,4	MCF-7	breast:
8	chr3:134091204..134095146-chr3:134189472..134194570,7	MCF-7	breast:
9	chr3:134191815..134194495-chr3:134200206..134203581,3	K562	blood:
10	chr3:134027069..134028938-chr3:134191393..134194235,2	MCF-7	breast:
11	chr3:134172461..134174570-chr3:134191518..134193817,2	MCF-7	breast:
12	chr3:134070789..134073283-chr3:134191774..134193534,2	MCF-7	breast:
13	chr3:134032191..134034661-chr3:134191037..134192947,2	MCF-7	breast:
14	chr3:134083001..134085504-chr3:134191468..134193210,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240006	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000214289	Chromatin interaction

Extended variants
information (count: 209 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:205)

rs_ID	r²[population]
rs10935113	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935120	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1138273	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes]
rs11706117	0.93[EUR][1000 genomes]
rs11708531	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11915964	0.91[CEU][hapmap]
rs11919350	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes]
rs11927068	0.91[EUR][1000 genomes]
rs11928499	0.92[EUR][1000 genomes]
rs12490835	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs12492930	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12637301	0.84[CEU][hapmap]
rs12637751	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs13059720	0.92[EUR][1000 genomes]
rs13064209	0.81[CEU][hapmap]
rs13065405	0.92[EUR][1000 genomes]
rs13065773	0.89[EUR][1000 genomes]
rs13075117	0.81[CEU][hapmap]
rs13075253	0.81[CEU][hapmap]
rs13076825	0.80[CEU][hapmap]
rs13081177	0.87[EUR][1000 genomes]
rs13081688	0.91[EUR][1000 genomes]
rs13084192	0.81[CEU][hapmap]
rs13087875	0.92[EUR][1000 genomes]
rs13089566	0.92[CEU][hapmap]
rs13089966	0.89[EUR][1000 genomes]
rs13096604	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs13098546	0.81[CEU][hapmap]
rs13316205	0.92[EUR][1000 genomes]
rs1357762	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1357764	0.92[CEU][hapmap]
rs1498718	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1534025	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs1534026	0.88[EUR][1000 genomes]
rs1534027	0.88[EUR][1000 genomes]
rs1534028	0.88[EUR][1000 genomes]
rs1534030	0.83[CEU][hapmap]
rs17694011	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1814336	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1814337	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1863912	0.91[EUR][1000 genomes]
rs1863913	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1874883	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1880375	0.84[CEU][hapmap]
rs1880376	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1880377	0.91[EUR][1000 genomes]
rs1917130	0.95[CEU][hapmap];0.85[YRI][hapmap]
rs2056603	1.00[CEU][hapmap]
rs2177601	0.92[EUR][1000 genomes]
rs2177602	0.91[EUR][1000 genomes]
rs2241556	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293293	0.87[CEU][hapmap]
rs2293294	0.84[CEU][hapmap];0.96[YRI][hapmap]
rs2370578	0.93[EUR][1000 genomes]
rs2370641	0.93[EUR][1000 genomes]
rs2370642	0.93[EUR][1000 genomes]
rs2373865	0.89[EUR][1000 genomes]
rs28409322	0.92[EUR][1000 genomes]
rs28702610	0.86[EUR][1000 genomes]
rs2887797	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2888670	0.83[CEU][hapmap];0.80[YRI][hapmap]
rs34029813	0.83[EUR][1000 genomes]
rs35718987	0.89[EUR][1000 genomes]
rs35933983	0.90[EUR][1000 genomes]
rs36006513	0.89[EUR][1000 genomes]
rs3846055	0.93[EUR][1000 genomes]
rs3846056	0.93[EUR][1000 genomes]
rs3856729	0.93[EUR][1000 genomes]
rs3932818	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs4074521	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs4074522	0.87[CEU][hapmap]
rs4245903	0.87[CEU][hapmap]
rs4245905	0.80[CEU][hapmap]
rs4245907	0.92[CEU][hapmap]
rs4306899	0.84[JPT][hapmap]
rs4309773	0.88[EUR][1000 genomes]
rs4367113	0.88[EUR][1000 genomes]
rs4417907	0.89[EUR][1000 genomes]
rs4435682	0.92[CEU][hapmap]
rs4498009	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4539979	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4572812	0.87[EUR][1000 genomes]
rs4634170	0.83[CEU][hapmap]
rs4955525	0.87[CEU][hapmap]
rs4955526	0.87[CEU][hapmap]
rs4955534	0.84[CEU][hapmap]
rs4955542	0.84[CEU][hapmap]
rs4955546	0.83[CEU][hapmap]
rs4955547	0.83[CEU][hapmap]
rs4955555	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4974478	0.88[EUR][1000 genomes]
rs4974480	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4974481	0.91[EUR][1000 genomes]
rs4974483	0.93[EUR][1000 genomes]
rs4974484	0.93[EUR][1000 genomes]
rs4974493	0.93[EUR][1000 genomes]
rs55913793	0.88[EUR][1000 genomes]
rs62269547	0.93[EUR][1000 genomes]
rs6439484	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6439487	0.91[EUR][1000 genomes]
rs6439492	0.81[EUR][1000 genomes]
rs6763088	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6763093	0.91[EUR][1000 genomes]
rs6763188	0.91[CEU][hapmap]
rs6764764	0.83[CEU][hapmap]
rs6765505	0.93[EUR][1000 genomes]
rs6766818	0.93[EUR][1000 genomes]
rs6766897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768323	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6769885	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6772406	0.93[EUR][1000 genomes]
rs6772896	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6775611	0.91[CEU][hapmap]
rs6776203	0.91[EUR][1000 genomes]
rs6779326	0.81[CEU][hapmap]
rs6782128	0.88[EUR][1000 genomes]
rs6785027	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6787371	0.91[EUR][1000 genomes]
rs6790338	0.93[EUR][1000 genomes]
rs6790466	0.93[EUR][1000 genomes]
rs6799110	0.93[EUR][1000 genomes]
rs6799543	0.93[EUR][1000 genomes]
rs6800862	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs6801596	0.91[EUR][1000 genomes]
rs6802654	0.93[EUR][1000 genomes]
rs6804770	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6805388	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6806417	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6806810	0.85[CEU][hapmap]
rs7356093	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7371896	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7372770	0.82[EUR][1000 genomes]
rs7373874	0.91[EUR][1000 genomes]
rs7374158	0.90[EUR][1000 genomes]
rs7374325	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7427492	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7428326	0.91[EUR][1000 genomes]
rs7429866	0.92[EUR][1000 genomes]
rs7430034	0.84[CEU][hapmap]
rs7432268	0.92[EUR][1000 genomes]
rs7433663	0.91[EUR][1000 genomes]
rs7611828	0.90[EUR][1000 genomes]
rs7619451	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs7623567	0.92[CEU][hapmap]
rs7626557	0.88[CEU][hapmap]
rs7627654	0.80[EUR][1000 genomes]
rs7627726	0.89[EUR][1000 genomes]
rs7630874	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs7637227	0.90[EUR][1000 genomes]
rs7648990	0.91[EUR][1000 genomes]
rs7649910	0.84[EUR][1000 genomes]
rs7653807	0.91[CEU][hapmap]
rs9289471	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9289475	0.91[EUR][1000 genomes]
rs9289476	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9289478	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs934093	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9809619	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9813774	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9814567	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs9815297	0.93[EUR][1000 genomes]
rs9815894	0.88[EUR][1000 genomes]
rs9815983	0.93[EUR][1000 genomes]
rs9819532	0.88[EUR][1000 genomes]
rs9820150	0.92[EUR][1000 genomes]
rs9820425	0.92[EUR][1000 genomes]
rs9824185	0.85[CEU][hapmap]
rs9826496	0.93[EUR][1000 genomes]
rs9827672	0.87[EUR][1000 genomes]
rs9827987	0.89[EUR][1000 genomes]
rs9828815	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9829092	0.92[EUR][1000 genomes]
rs9832785	0.93[EUR][1000 genomes]
rs9833753	0.93[EUR][1000 genomes]
rs9834755	0.93[EUR][1000 genomes]
rs9835204	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9836401	0.81[CEU][hapmap]
rs9838119	0.81[CEU][hapmap]
rs9838467	0.81[CEU][hapmap]
rs9838834	0.93[EUR][1000 genomes]
rs9841212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841371	0.88[CEU][hapmap]
rs9844537	0.91[EUR][1000 genomes]
rs9847788	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs9848254	0.81[CEU][hapmap]
rs9850015	0.91[EUR][1000 genomes]
rs9851441	1.00[CEU][hapmap]
rs9854299	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9855013	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9857242	0.87[CEU][hapmap]
rs9857995	0.87[CEU][hapmap]
rs9863786	0.90[EUR][1000 genomes]
rs9864346	1.00[CEU][hapmap]
rs9869981	0.93[EUR][1000 genomes]
rs9870262	0.90[EUR][1000 genomes]
rs9871226	0.81[CEU][hapmap]
rs9871305	0.93[EUR][1000 genomes]
rs9876658	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9883753	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9884031	0.91[EUR][1000 genomes]
rs9968172	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs9985341	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9985356	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9989967	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9990351	1.00[CEU][hapmap];0.91[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:27)

SNP	Gene	Cis/trans	Tissue	Source
rs9841180	CEP63	cis	Esophagus Mucosa	GTEx
rs9841180	CEP63	cis	lesional skin	skin_eQTL
rs9841180	CEP63	cis	lung	GTEx
rs9841180	ANAPC13	cis	uninvolved skin	skin_eQTL
rs9841180	ANAPC13	cis	Heart Left Ventricle	GTEx
rs9841180	CEP63	cis	Artery Tibial	GTEx
rs9841180	CEP63	cis	Esophagus Muscularis	GTEx
rs9841180	ANAPC13	cis	Whole Blood	GTEx
rs9841180	ANAPC13	cis	Esophagus Muscularis	GTEx
rs9841180	ANAPC13	cis	Artery Aorta	GTEx
rs9841180	CEP63	cis	Muscle Skeletal	GTEx
rs9841180	CEP63	cis	Nerve Tibial	GTEx
rs9841180	ANAPC13	cis	multi-tissue	Pritchard
rs9841180	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs9841180	ANAPC13	cis	Artery Tibial	GTEx
rs9841180	ANAPC13	cis	normal skin	skin_eQTL
rs9841180	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs9841180	ANAPC13	cis	Esophagus Mucosa	GTEx
rs9841180	ANAPC13	cis	lung	GTEx
rs9841180	ANAPC13	cis	lesional skin	skin_eQTL
rs9841180	ANAPC13	cis	Thyroid	GTEx
rs9841180	ANAPC13	cis	Muscle Skeletal	GTEx
rs9841180	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs9841180	ANAPC13	cis	Nerve Tibial	GTEx
rs9841180	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs9841180	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs9841180	ANAPC13	cis	Stomach	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134181800-134195000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:134182400-134195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:134182800-134195200	Weak transcription	Colonic Mucosa	Colon
4	chr3:134182800-134195400	Weak transcription	Small Intestine	intestine
5	chr3:134182800-134199400	Weak transcription	Pancreas	Pancrea
6	chr3:134183600-134195000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:134183800-134192600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:134183800-134195000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:134183800-134195800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:134183800-134203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:134184000-134192600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:134184000-134192600	Weak transcription	Psoas Muscle	Psoas
13	chr3:134184000-134192600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:134184000-134193800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:134184000-134197000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:134184000-134197000	Weak transcription	Ovary	ovary
17	chr3:134184000-134199400	Weak transcription	Aorta	Aorta
18	chr3:134184000-134203000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:134184200-134192600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:134184200-134194600	Weak transcription	Brain Germinal Matrix	brain
21	chr3:134184600-134195600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:134185200-134192600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:134185400-134194800	Weak transcription	Fetal Brain Female	brain
24	chr3:134185600-134194200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:134186000-134197000	Weak transcription	Fetal Brain Male	brain
26	chr3:134186800-134192600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:134186800-134195000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:134186800-134195200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:134187600-134192600	Weak transcription	HepG2	liver
30	chr3:134187600-134195000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:134187800-134192600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:134188000-134192600	Weak transcription	Fetal Intestine Small	intestine
33	chr3:134188200-134195000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:134188800-134193800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:134189000-134192000	Enhancers	Stomach Mucosa	stomach
36	chr3:134189000-134192600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:134189000-134193000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:134189200-134192600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:134189200-134195600	Weak transcription	Thymus	Thymus
40	chr3:134189600-134194400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:134190000-134192600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:134190000-134193600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:134190000-134194400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:134190000-134195000	Weak transcription	GM12878-XiMat	blood
45	chr3:134190200-134192200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:134190200-134192400	Strong transcription	Primary T cells from cord blood	blood
47	chr3:134190200-134192600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:134190200-134193000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:134190400-134192000	Enhancers	Lung	lung
50	chr3:134190400-134192200	Strong transcription	Primary B cells from cord blood	blood

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