Variant report

Variant	rs10142878
Chromosome Location	chr14:67412419-67412420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:67406512..67408916-chr14:67410508..67412779,2	MCF-7	breast:

Extended variants
information (count: 198 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs10047902	0.84[ASN][1000 genomes]
rs10047906	0.86[ASN][1000 genomes]
rs10130604	0.83[ASN][1000 genomes]
rs10131242	0.83[ASN][1000 genomes]
rs10132565	0.95[ASN][1000 genomes]
rs10132625	0.81[ASN][1000 genomes]
rs10133107	0.80[ASN][1000 genomes]
rs10135100	0.84[ASN][1000 genomes]
rs10135117	0.95[ASN][1000 genomes]
rs10135674	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10135701	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10136026	0.95[ASN][1000 genomes]
rs10136043	0.89[ASN][1000 genomes]
rs10136344	0.95[ASN][1000 genomes]
rs10137618	0.83[ASN][1000 genomes]
rs10138631	0.83[ASN][1000 genomes]
rs10138952	0.83[ASN][1000 genomes]
rs10140569	0.86[ASN][1000 genomes]
rs10141815	0.84[ASN][1000 genomes]
rs10141947	0.82[ASN][1000 genomes]
rs10142152	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10142176	0.86[ASN][1000 genomes]
rs10143670	0.81[AMR][1000 genomes]
rs10144915	0.85[ASN][1000 genomes]
rs10146304	0.83[ASN][1000 genomes]
rs10147954	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10148117	0.93[ASN][1000 genomes]
rs10149600	0.81[ASN][1000 genomes]
rs10149760	0.84[ASN][1000 genomes]
rs10150098	0.97[ASN][1000 genomes]
rs10150145	0.83[ASN][1000 genomes]
rs10150424	0.83[ASN][1000 genomes]
rs10151405	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10151487	0.92[ASN][1000 genomes]
rs10162330	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10220477	0.86[ASN][1000 genomes]
rs1080053	0.85[ASN][1000 genomes]
rs10873197	0.95[ASN][1000 genomes]
rs10873198	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11158647	0.81[ASN][1000 genomes]
rs11158649	0.95[ASN][1000 genomes]
rs11158650	0.88[ASN][1000 genomes]
rs11158651	0.83[ASN][1000 genomes]
rs1138802	0.88[ASN][1000 genomes]
rs12323781	0.83[ASN][1000 genomes]
rs12587989	0.87[ASN][1000 genomes]
rs12588821	0.93[ASN][1000 genomes]
rs12590085	0.82[ASN][1000 genomes]
rs13379445	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13379476	0.95[ASN][1000 genomes]
rs13379478	0.97[ASN][1000 genomes]
rs1546940	0.81[ASN][1000 genomes]
rs17247862	0.86[ASN][1000 genomes]
rs17836604	0.81[ASN][1000 genomes]
rs1884066	0.92[ASN][1000 genomes]
rs1950281	0.92[ASN][1000 genomes]
rs1950282	0.81[ASN][1000 genomes]
rs1950284	0.81[ASN][1000 genomes]
rs1950689	0.81[ASN][1000 genomes]
rs1955604	0.92[ASN][1000 genomes]
rs1955606	0.80[ASN][1000 genomes]
rs1955608	0.84[ASN][1000 genomes]
rs1955609	0.84[ASN][1000 genomes]
rs1955610	0.84[ASN][1000 genomes]
rs1957297	0.87[ASN][1000 genomes]
rs2013137	0.91[ASN][1000 genomes]
rs2038398	0.94[ASN][1000 genomes]
rs2064489	0.80[ASN][1000 genomes]
rs2064777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2144909	0.86[ASN][1000 genomes]
rs2319549	0.94[ASN][1000 genomes]
rs28398007	0.94[ASN][1000 genomes]
rs28444104	0.85[ASN][1000 genomes]
rs28539317	0.81[ASN][1000 genomes]
rs28668670	0.81[ASN][1000 genomes]
rs28673894	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28685619	0.83[ASN][1000 genomes]
rs28718312	0.84[ASN][1000 genomes]
rs28762177	0.84[ASN][1000 genomes]
rs28817965	0.94[ASN][1000 genomes]
rs28828116	0.84[ASN][1000 genomes]
rs28850894	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3752993	0.85[ASN][1000 genomes]
rs3784074	0.85[ASN][1000 genomes]
rs3784075	0.86[ASN][1000 genomes]
rs4141702	0.85[ASN][1000 genomes]
rs4141703	0.87[ASN][1000 genomes]
rs56094582	0.82[ASN][1000 genomes]
rs56189117	0.81[ASN][1000 genomes]
rs58367317	0.95[ASN][1000 genomes]
rs59774616	0.84[ASN][1000 genomes]
rs60550390	0.89[ASN][1000 genomes]
rs60656960	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61029022	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61386326	0.84[ASN][1000 genomes]
rs6573720	0.81[ASN][1000 genomes]
rs6573726	0.85[ASN][1000 genomes]
rs6573727	0.85[ASN][1000 genomes]
rs6573728	0.84[ASN][1000 genomes]
rs6573729	0.86[ASN][1000 genomes]
rs6573732	0.85[ASN][1000 genomes]
rs6573733	0.85[ASN][1000 genomes]
rs6573734	0.88[ASN][1000 genomes]
rs6573735	0.92[ASN][1000 genomes]
rs6573736	0.90[ASN][1000 genomes]
rs6573737	0.92[ASN][1000 genomes]
rs6573740	0.92[ASN][1000 genomes]
rs6573741	0.93[ASN][1000 genomes]
rs6573742	0.88[ASN][1000 genomes]
rs6573744	0.83[ASN][1000 genomes]
rs6573745	0.80[ASN][1000 genomes]
rs6573746	0.82[ASN][1000 genomes]
rs6573747	0.82[ASN][1000 genomes]
rs6573748	0.81[ASN][1000 genomes]
rs6573749	0.85[ASN][1000 genomes]
rs6573750	0.84[ASN][1000 genomes]
rs68178754	0.92[ASN][1000 genomes]
rs7141519	0.83[ASN][1000 genomes]
rs7142068	0.90[ASN][1000 genomes]
rs7144434	0.83[ASN][1000 genomes]
rs7144580	0.83[ASN][1000 genomes]
rs7145226	0.81[ASN][1000 genomes]
rs7145295	0.80[ASN][1000 genomes]
rs7145718	0.85[ASN][1000 genomes]
rs7145844	0.95[ASN][1000 genomes]
rs7145917	0.89[ASN][1000 genomes]
rs7146098	0.92[ASN][1000 genomes]
rs7146635	0.92[ASN][1000 genomes]
rs7147570	0.92[ASN][1000 genomes]
rs7147943	0.84[ASN][1000 genomes]
rs7148911	0.87[ASN][1000 genomes]
rs7149711	0.81[ASN][1000 genomes]
rs7149905	0.80[ASN][1000 genomes]
rs7150131	0.81[ASN][1000 genomes]
rs7150739	0.83[ASN][1000 genomes]
rs7151086	0.82[ASN][1000 genomes]
rs7152001	0.88[ASN][1000 genomes]
rs7152422	0.92[ASN][1000 genomes]
rs7153936	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7155042	0.86[ASN][1000 genomes]
rs7156081	0.94[ASN][1000 genomes]
rs7156655	0.85[ASN][1000 genomes]
rs7156852	0.87[ASN][1000 genomes]
rs7157126	0.81[ASN][1000 genomes]
rs7158760	0.89[ASN][1000 genomes]
rs7159871	0.84[ASN][1000 genomes]
rs7160476	0.87[ASN][1000 genomes]
rs7161664	0.83[ASN][1000 genomes]
rs7161698	0.86[ASN][1000 genomes]
rs723432	0.90[ASN][1000 genomes]
rs728647	0.90[ASN][1000 genomes]
rs73274960	0.85[ASN][1000 genomes]
rs8003434	0.88[ASN][1000 genomes]
rs8003929	0.82[ASN][1000 genomes]
rs8005668	0.94[ASN][1000 genomes]
rs8006067	0.87[ASN][1000 genomes]
rs8006552	0.81[ASN][1000 genomes]
rs8006669	0.82[ASN][1000 genomes]
rs8008739	0.86[ASN][1000 genomes]
rs8008773	0.82[ASN][1000 genomes]
rs8012063	0.92[ASN][1000 genomes]
rs8012660	0.85[ASN][1000 genomes]
rs8012944	0.83[ASN][1000 genomes]
rs8013401	0.92[ASN][1000 genomes]
rs8013943	0.92[ASN][1000 genomes]
rs8014841	0.84[ASN][1000 genomes]
rs8016186	0.85[ASN][1000 genomes]
rs8016391	0.83[ASN][1000 genomes]
rs8016725	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8018545	0.81[ASN][1000 genomes]
rs8018750	0.91[ASN][1000 genomes]
rs8018920	0.85[ASN][1000 genomes]
rs8019510	0.83[ASN][1000 genomes]
rs8020095	0.90[ASN][1000 genomes]
rs8020144	0.83[ASN][1000 genomes]
rs8021044	0.89[ASN][1000 genomes]
rs8021795	0.82[ASN][1000 genomes]
rs8022437	0.86[ASN][1000 genomes]
rs8022657	0.92[ASN][1000 genomes]
rs9323485	0.81[ASN][1000 genomes]
rs9323486	0.85[ASN][1000 genomes]
rs9323488	0.83[ASN][1000 genomes]
rs9323489	0.84[ASN][1000 genomes]
rs9323490	0.83[ASN][1000 genomes]
rs9323491	0.83[ASN][1000 genomes]
rs9323492	0.83[ASN][1000 genomes]
rs9323493	0.80[ASN][1000 genomes]
rs9671368	0.82[ASN][1000 genomes]
rs9743488	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385263	chr14:66514718-67511481	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv525460	chr14:66851185-67626594	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv1834170	chr14:67103140-67527235	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2829998	chr14:67103579-67626594	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1838724	chr14:67232573-67527235	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2763071	chr14:67284476-67597237	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv902058	chr14:67310195-67760538	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv902059	chr14:67352226-67760538	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10142878	ATP6V1D	cis	lung	GTEx
rs10142878	ATP6V1D	cis	Thyroid	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67405200-67416400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr14:67405800-67416400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr14:67406000-67414600	ZNF genes & repeats	Liver	Liver
4	chr14:67406000-67416200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr14:67406200-67414600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr14:67406200-67416400	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr14:67408400-67414200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr14:67408400-67414600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:67409000-67414000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:67409000-67414000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:67409800-67413600	ZNF genes & repeats	GM12878-XiMat	blood
12	chr14:67409800-67414000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr14:67410000-67412600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr14:67410000-67412600	ZNF genes & repeats	NHEK	skin
15	chr14:67410000-67412800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:67410000-67414600	ZNF genes & repeats	Brain Hippocampus Middle	brain
17	chr14:67410200-67414200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:67410200-67414800	ZNF genes & repeats	Brain Anterior Caudate	brain
19	chr14:67410200-67415800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr14:67410600-67413400	ZNF genes & repeats	Left Ventricle	heart
21	chr14:67410600-67414600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr14:67410800-67412800	ZNF genes & repeats	Brain Substantia Nigra	brain
23	chr14:67410800-67414600	ZNF genes & repeats	Dnd41	blood
24	chr14:67411000-67413400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:67411000-67413400	ZNF genes & repeats	Right Ventricle	heart
26	chr14:67411000-67414800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
27	chr14:67411400-67413000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:67411400-67413200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:67411400-67413600	ZNF genes & repeats	Ovary	ovary
30	chr14:67411400-67413800	ZNF genes & repeats	Fetal Brain Male	brain
31	chr14:67411400-67414200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr14:67411400-67414600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
33	chr14:67411600-67412600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr14:67411600-67413800	ZNF genes & repeats	Fetal Brain Female	brain
35	chr14:67411600-67414600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
36	chr14:67411600-67414600	ZNF genes & repeats	Fetal Lung	lung
37	chr14:67411600-67414600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
38	chr14:67412000-67415200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:67412200-67413000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr14:67412200-67413000	Weak transcription	Fetal Stomach	stomach
41	chr14:67412200-67413000	Weak transcription	Lung	lung
42	chr14:67412200-67413200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:67412200-67413200	Weak transcription	Aorta	Aorta
44	chr14:67412200-67413600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:67412200-67414000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr14:67412200-67414400	Weak transcription	Pancreas	Pancrea
47	chr14:67412200-67414600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr14:67412200-67417600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr14:67412200-67425000	Weak transcription	Gastric	stomach
50	chr14:67412200-67425800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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