Variant report

Variant	rs9847788
Chromosome Location	chr3:134186496-134186497
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134071281..134073530-chr3:134186337..134189108,2	MCF-7	breast:
2	chr3:134179371..134182276-chr3:134185346..134188135,2	K562	blood:
3	chr3:134185236..134187587-chr3:134203090..134205946,3	MCF-7	breast:
4	chr3:134183286..134186768-chr3:134202310..134205275,3	K562	blood:

Variant related genes	Relation type
ENSG00000129055	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10935120	1.00[CEU][hapmap]
rs1138273	1.00[CEU][hapmap]
rs11708531	1.00[CEU][hapmap]
rs11915964	0.91[CEU][hapmap]
rs11919350	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs12490835	0.96[CEU][hapmap]
rs12492930	1.00[CEU][hapmap]
rs12637301	0.84[CEU][hapmap]
rs12637751	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs13064209	0.82[CEU][hapmap]
rs13075117	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs13075253	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs13076825	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs13084192	0.82[CEU][hapmap]
rs13089566	0.92[CEU][hapmap]
rs13096604	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs13098546	0.82[CEU][hapmap]
rs1357762	1.00[CEU][hapmap]
rs1357764	0.92[CEU][hapmap]
rs1366067	0.82[CHB][hapmap]
rs1391695	0.83[CHB][hapmap]
rs1498718	1.00[CEU][hapmap]
rs1534025	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1534030	0.83[CEU][hapmap]
rs17694011	0.96[CEU][hapmap]
rs1814336	1.00[CEU][hapmap]
rs1814337	0.96[CEU][hapmap]
rs1863913	1.00[CEU][hapmap]
rs1874883	1.00[CEU][hapmap]
rs1880375	0.85[CEU][hapmap]
rs1880376	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1917130	0.95[CEU][hapmap]
rs2056603	1.00[CEU][hapmap]
rs2241556	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2293293	0.88[CEU][hapmap]
rs2293294	0.84[CEU][hapmap]
rs2887797	1.00[CEU][hapmap]
rs2888670	0.84[CEU][hapmap]
rs3932818	0.96[CEU][hapmap]
rs4074521	0.88[CEU][hapmap]
rs4074522	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs4245903	0.88[CEU][hapmap]
rs4245905	0.81[CEU][hapmap]
rs4245907	0.92[CEU][hapmap]
rs4435682	0.92[CEU][hapmap]
rs4498009	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs4539979	1.00[CEU][hapmap]
rs4543053	0.80[CEU][hapmap]
rs4634170	0.84[CEU][hapmap]
rs4955525	0.88[CEU][hapmap]
rs4955526	0.88[CEU][hapmap]
rs4955534	0.84[CEU][hapmap]
rs4955542	0.84[CEU][hapmap]
rs4955546	0.83[CEU][hapmap]
rs4955547	0.84[CEU][hapmap]
rs4955555	1.00[CEU][hapmap]
rs4974480	0.96[CEU][hapmap]
rs6439484	1.00[CEU][hapmap]
rs6763088	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs6763188	0.92[CEU][hapmap]
rs6764764	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs6766897	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs6768323	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs6769885	0.96[CEU][hapmap]
rs6772896	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs6775611	0.91[CEU][hapmap]
rs6779326	0.82[CEU][hapmap]
rs6785027	1.00[CEU][hapmap]
rs6790466	0.85[YRI][hapmap]
rs6800862	0.96[CEU][hapmap]
rs6804770	1.00[CEU][hapmap]
rs6805388	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6806417	1.00[CEU][hapmap]
rs6806810	0.85[CEU][hapmap]
rs7356093	1.00[CEU][hapmap]
rs7371896	1.00[CEU][hapmap]
rs7374325	1.00[CEU][hapmap]
rs7427492	1.00[CEU][hapmap]
rs7430034	0.84[CEU][hapmap]
rs7619451	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs7623567	0.92[CEU][hapmap]
rs7626557	0.88[CEU][hapmap]
rs7630874	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs7650509	0.82[CHB][hapmap]
rs7653807	0.91[CEU][hapmap]
rs9289471	1.00[CEU][hapmap]
rs9289476	1.00[CEU][hapmap]
rs9289478	1.00[CEU][hapmap]
rs934093	0.91[CEU][hapmap]
rs9809344	0.80[CEU][hapmap]
rs9809619	1.00[CEU][hapmap]
rs9813774	1.00[CEU][hapmap]
rs9814567	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs9824185	0.85[CEU][hapmap]
rs9828815	1.00[CEU][hapmap]
rs9835204	1.00[CEU][hapmap]
rs9836401	0.82[CEU][hapmap]
rs9838119	0.82[CEU][hapmap]
rs9838467	0.82[CEU][hapmap]
rs9841180	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs9841212	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9841371	0.88[CEU][hapmap]
rs9848254	0.82[CEU][hapmap]
rs9851441	1.00[CEU][hapmap]
rs9854299	1.00[CEU][hapmap]
rs9855013	1.00[CEU][hapmap]
rs9857242	0.88[CEU][hapmap]
rs9857995	0.88[CEU][hapmap]
rs9864346	1.00[CEU][hapmap]
rs9871226	0.81[CEU][hapmap]
rs9876658	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9883753	1.00[CEU][hapmap]
rs9968172	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs9985341	1.00[CEU][hapmap]
rs9985356	1.00[CEU][hapmap]
rs9989967	1.00[CEU][hapmap]
rs9990351	1.00[CEU][hapmap]

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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs9847788	CEP63	cis	Muscle Skeletal	GTEx
rs9847788	ANAPC13	cis	uninvolved skin	skin_eQTL
rs9847788	ANAPC13	cis	multi-tissue	Pritchard
rs9847788	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs9847788	ANAPC13	cis	Artery Tibial	GTEx
rs9847788	ANAPC13	cis	Stomach	GTEx
rs9847788	ANAPC13	cis	Esophagus Muscularis	GTEx
rs9847788	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs9847788	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs9847788	CEP63	cis	Artery Tibial	GTEx
rs9847788	CEP63	cis	Esophagus Mucosa	GTEx
rs9847788	ANAPC13	cis	normal skin	skin_eQTL
rs9847788	ANAPC13	cis	lung	GTEx
rs9847788	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs9847788	CEP63	cis	lesional skin	skin_eQTL
rs9847788	CEP63	cis	Esophagus Muscularis	GTEx
rs9847788	ANAPC13	cis	lesional skin	skin_eQTL
rs9847788	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs9847788	ANAPC13	cis	Esophagus Mucosa	GTEx
rs9847788	ANAPC13	cis	Nerve Tibial	GTEx
rs9847788	ANAPC13	cis	Muscle Skeletal	GTEx
rs9847788	ANAPC13	cis	Thyroid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134180800-134186600	Enhancers	Fetal Stomach	stomach
2	chr3:134181400-134189400	Weak transcription	A549	lung
3	chr3:134181400-134190400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:134181800-134195000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:134182200-134190200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:134182400-134195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:134182800-134190000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:134182800-134190800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:134182800-134195200	Weak transcription	Colonic Mucosa	Colon
10	chr3:134182800-134195400	Weak transcription	Small Intestine	intestine
11	chr3:134182800-134199400	Weak transcription	Pancreas	Pancrea
12	chr3:134183600-134195000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:134183800-134186600	Enhancers	Fetal Lung	lung
14	chr3:134183800-134186800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:134183800-134187400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:134183800-134187400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:134183800-134192600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:134183800-134195000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:134183800-134195800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:134183800-134203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:134184000-134186800	Enhancers	NHLF	lung
22	chr3:134184000-134187200	Enhancers	NHDF-Ad	bronchial
23	chr3:134184000-134189600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:134184000-134190200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:134184000-134190200	Weak transcription	HSMM	muscle
26	chr3:134184000-134190400	Weak transcription	HSMMtube	muscle
27	chr3:134184000-134190600	Weak transcription	Spleen	Spleen
28	chr3:134184000-134192600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:134184000-134192600	Weak transcription	Psoas Muscle	Psoas
30	chr3:134184000-134192600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:134184000-134193800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:134184000-134197000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:134184000-134197000	Weak transcription	Ovary	ovary
34	chr3:134184000-134199400	Weak transcription	Aorta	Aorta
35	chr3:134184000-134203000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:134184200-134189400	Weak transcription	NH-A	brain
37	chr3:134184200-134190200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:134184200-134190400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:134184200-134191200	Weak transcription	Fetal Kidney	kidney
40	chr3:134184200-134192600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:134184200-134194600	Weak transcription	Brain Germinal Matrix	brain
42	chr3:134184600-134190400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:134184600-134195600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:134184800-134187000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:134185200-134192600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:134185400-134194800	Weak transcription	Fetal Brain Female	brain
47	chr3:134185600-134186800	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:134185600-134194200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:134185800-134190200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:134185800-134190200	Weak transcription	Primary T cells from cord blood	blood

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