Variant report

Variant	rs10140679
Chromosome Location	chr14:63901294-63901295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:63899201..63902873-chr14:64106888..64109598,3	K562	blood:
2	chr14:63894929..63897149-chr14:63899211..63901450,2	MCF-7	breast:
3	chr14:63900892..63902977-chr14:63913648..63915653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140006	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1012145	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10129170	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10130074	0.89[ASN][1000 genomes]
rs10132996	0.89[ASN][1000 genomes]
rs10133014	0.89[ASN][1000 genomes]
rs10137243	0.90[ASN][1000 genomes]
rs10137259	0.89[ASN][1000 genomes]
rs10137279	0.92[ASN][1000 genomes]
rs10138187	0.93[ASN][1000 genomes]
rs10138274	0.93[ASN][1000 genomes]
rs10138372	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10138832	0.92[ASN][1000 genomes]
rs10139725	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10140710	0.87[ASN][1000 genomes]
rs10140718	0.86[ASN][1000 genomes]
rs10141179	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10144700	0.93[ASN][1000 genomes]
rs10146848	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10148185	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10149549	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10151527	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs1033742	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1033744	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10483773	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11158491	0.86[CEU][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11850626	0.83[ASN][1000 genomes]
rs12323479	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12434321	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1475040	0.89[ASN][1000 genomes]
rs17093492	0.93[ASN][1000 genomes]
rs17101205	0.93[ASN][1000 genomes]
rs17101207	0.93[ASN][1000 genomes]
rs17225252	0.93[ASN][1000 genomes]
rs17225266	0.92[ASN][1000 genomes]
rs17825105	0.93[ASN][1000 genomes]
rs1951212	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1951213	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1957045	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs28496722	0.94[ASN][1000 genomes]
rs28522688	0.89[ASN][1000 genomes]
rs28560307	0.92[ASN][1000 genomes]
rs28592209	0.93[ASN][1000 genomes]
rs28620591	0.93[ASN][1000 genomes]
rs28696283	0.89[ASN][1000 genomes]
rs28711489	0.90[ASN][1000 genomes]
rs3783741	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3783743	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4899113	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4902226	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4902227	0.94[ASN][1000 genomes]
rs55859128	0.81[ASN][1000 genomes]
rs57760311	0.87[ASN][1000 genomes]
rs60644154	0.90[ASN][1000 genomes]
rs61627079	0.87[ASN][1000 genomes]
rs6573520	0.93[ASN][1000 genomes]
rs7144120	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7146069	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7152839	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7153764	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7154559	0.94[ASN][1000 genomes]
rs7161634	0.94[ASN][1000 genomes]
rs8003115	0.93[ASN][1000 genomes]
rs8003246	0.94[ASN][1000 genomes]
rs8004170	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs8007996	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs8008684	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8014486	0.85[ASN][1000 genomes]
rs8016306	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs8018107	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527251	chr14:63400786-64068806	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv520528	chr14:63400786-64157117	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv530774	chr14:63591348-64029881	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv832815	chr14:63750058-63913900	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10140679	WDR89	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:63837800-63902200	Weak transcription	Small Intestine	intestine
2	chr14:63851200-63902400	Weak transcription	Right Ventricle	heart
3	chr14:63851200-63903600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:63851200-63922000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:63854800-63922400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:63859800-63901600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr14:63862000-63902200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:63862200-63902600	Weak transcription	Brain Angular Gyrus	brain
9	chr14:63862200-63903600	Weak transcription	HMEC	breast
10	chr14:63877400-63903200	Weak transcription	Aorta	Aorta
11	chr14:63877800-63901600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:63880800-63902000	Weak transcription	NHLF	lung
13	chr14:63880800-63902600	Weak transcription	Lung	lung
14	chr14:63880800-63904400	Weak transcription	NHEK	skin
15	chr14:63881400-63902200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr14:63886000-63902000	Weak transcription	Fetal Intestine Small	intestine
17	chr14:63887400-63918600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr14:63887400-63918800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr14:63888200-63902200	Weak transcription	Adipose Nuclei	Adipose
20	chr14:63888400-63902000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr14:63888400-63902200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr14:63888400-63902200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:63888600-63902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr14:63888600-63902200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr14:63888600-63903200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr14:63888600-63903600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr14:63888600-63904800	Weak transcription	Dnd41	blood
28	chr14:63888800-63902200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr14:63889000-63901400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr14:63889000-63902200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr14:63889000-63902400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:63889000-63902600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:63889000-63902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr14:63889000-63903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:63889000-63904400	Weak transcription	NH-A	brain
36	chr14:63889000-63905000	Weak transcription	Thymus	Thymus
37	chr14:63889200-63902000	Weak transcription	Fetal Muscle Leg	muscle
38	chr14:63889200-63902200	Weak transcription	Primary B cells from cord blood	blood
39	chr14:63889200-63902200	Weak transcription	Primary T cells from cord blood	blood
40	chr14:63889200-63902400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr14:63889200-63902600	Weak transcription	Fetal Brain Female	brain
42	chr14:63889200-63904200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr14:63892000-63905200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:63893800-63902600	Weak transcription	Fetal Brain Male	brain
45	chr14:63894600-63903600	Weak transcription	Spleen	Spleen
46	chr14:63898200-63903200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr14:63899000-63901400	Weak transcription	Stomach Mucosa	stomach
48	chr14:63899000-63901600	Enhancers	Brain Substantia Nigra	brain
49	chr14:63899400-63901400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:63899400-63901400	Weak transcription	Fetal Lung	lung

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