Variant report

Variant	rs10131625
Chromosome Location	chr14:35760888-35760889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr14:35760864-35761988	GM12878	blood:	n/a	n/a
2	TAF1	chr14:35760738-35762139	HepG2	liver:	n/a	n/a
3	REST	chr14:35760707-35762231	HepG2	liver:	n/a	chr14:35761962-35761975
4	POLR2A	chr14:35760858-35762086	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr14:35760866-35762449	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr14:35760868-35762665	GM12891	blood:	n/a	n/a
7	HEY1	chr14:35760650-35762305	HepG2	liver:	n/a	n/a
8	YY1	chr14:35760206-35761056	HepG2	liver:	n/a	n/a
9	MXI1	chr14:35760773-35763195	SK-N-SH	brain:	n/a	n/a
10	GABPA	chr14:35760849-35762672	MCF-7	breast:	n/a	chr14:35761446-35761457 chr14:35761443-35761457 chr14:35761446-35761460 chr14:35761499-35761508
11	MYBL2	chr14:35759796-35762243	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:35760811-35762246	K562	blood:	n/a	n/a
13	NRF1	chr14:35760863-35762026	SK-N-SH	brain:	n/a	chr14:35761446-35761457 chr14:35761443-35761457 chr14:35761445-35761456 chr14:35761446-35761460 chr14:35761499-35761508
14	FOSL2	chr14:35760623-35762274	HepG2	liver:	n/a	chr14:35761247-35761258
15	POLR2A	chr14:35760659-35761009	HepG2	liver:	n/a	n/a
16	POLR2A	chr14:35759856-35762272	HepG2	liver:	n/a	n/a
17	POLR2A	chr14:35760627-35762270	GM12892	blood:	n/a	n/a
18	MTA3	chr14:35760848-35762211	GM12878	blood:	n/a	n/a
19	POLR2A	chr14:35760720-35762712	HepG2	liver:	n/a	n/a
20	POLR2A	chr14:35760771-35762408	GM12892	blood:	n/a	n/a
21	YY1	chr14:35760628-35761883	HepG2	liver:	n/a	chr14:35761499-35761508
22	POLR2A	chr14:35759775-35762762	HepG2	liver:	n/a	n/a
23	POLR2A	chr14:35760701-35760999	HepG2	liver:	n/a	n/a
24	POLR2A	chr14:35760643-35762174	HepG2	liver:	n/a	n/a
25	HEY1	chr14:35759838-35762159	HepG2	liver:	n/a	n/a
26	POLR2A	chr14:35760675-35762218	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:35757780..35767592-chr14:35866063..35878024,53	MCF-7	breast:
2	chr14:35701633..35705447-chr14:35760005..35763215,4	MCF-7	breast:
3	chr14:35760513..35762912-chr14:35858124..35860393,3	K562	blood:
4	chr14:35760689..35762512-chr8:131454589..131456596,2	MCF-7	breast:
5	chr14:35757192..35766588-chr14:35865950..35877395,53	MCF-7	breast:

Variant related genes	Relation type
PSMA6	TF binding region
ENSG00000256243	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000153317	Chromatin interaction
ENSG00000240023	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10047949	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132920	1.00[ASN][1000 genomes]
rs10134308	1.00[ASN][1000 genomes]
rs10136978	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137019	1.00[ASN][1000 genomes]
rs10142846	1.00[ASN][1000 genomes]
rs10144857	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146133	0.85[ASN][1000 genomes]
rs10146691	0.96[ASN][1000 genomes]
rs10147645	0.96[ASN][1000 genomes]
rs10149823	0.93[ASN][1000 genomes]
rs1064248	1.00[ASN][1000 genomes]
rs11156874	0.85[ASN][1000 genomes]
rs11844031	0.96[ASN][1000 genomes]
rs11845183	0.96[ASN][1000 genomes]
rs11845364	1.00[ASN][1000 genomes]
rs11848309	0.85[ASN][1000 genomes]
rs11849461	0.96[ASN][1000 genomes]
rs11851820	0.96[ASN][1000 genomes]
rs11852178	0.96[ASN][1000 genomes]
rs12100582	1.00[ASN][1000 genomes]
rs12100980	1.00[ASN][1000 genomes]
rs12436351	0.96[ASN][1000 genomes]
rs17091807	0.85[ASN][1000 genomes]
rs17103111	0.93[ASN][1000 genomes]
rs17103147	1.00[ASN][1000 genomes]
rs17103166	0.96[ASN][1000 genomes]
rs17386684	0.85[ASN][1000 genomes]
rs17456067	0.85[ASN][1000 genomes]
rs1807162	0.85[ASN][1000 genomes]
rs1884715	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2145622	0.96[ASN][1000 genomes]
rs2277459	1.00[ASN][1000 genomes]
rs2277461	1.00[ASN][1000 genomes]
rs2415278	1.00[ASN][1000 genomes]
rs2415284	1.00[ASN][1000 genomes]
rs28470932	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504476	0.96[ASN][1000 genomes]
rs28505171	0.93[ASN][1000 genomes]
rs28595436	1.00[ASN][1000 genomes]
rs28665705	1.00[ASN][1000 genomes]
rs28708376	1.00[ASN][1000 genomes]
rs28736779	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899832	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509212	0.85[ASN][1000 genomes]
rs4494460	0.85[ASN][1000 genomes]
rs55907319	1.00[ASN][1000 genomes]
rs58064181	0.96[ASN][1000 genomes]
rs60940685	0.96[ASN][1000 genomes]
rs62625039	0.85[ASN][1000 genomes]
rs6571694	0.85[ASN][1000 genomes]
rs6571695	0.85[ASN][1000 genomes]
rs6571709	1.00[ASN][1000 genomes]
rs7148424	1.00[ASN][1000 genomes]
rs7149602	1.00[ASN][1000 genomes]
rs7153807	1.00[ASN][1000 genomes]
rs7154637	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155335	0.93[ASN][1000 genomes]
rs7218	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664840	0.85[ASN][1000 genomes]
rs72664843	0.85[ASN][1000 genomes]
rs72664854	0.85[ASN][1000 genomes]
rs72664855	0.85[ASN][1000 genomes]
rs73239026	0.96[ASN][1000 genomes]
rs73239030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73239072	1.00[ASN][1000 genomes]
rs73239074	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73240720	0.96[ASN][1000 genomes]
rs73240721	0.96[ASN][1000 genomes]
rs74043875	0.96[ASN][1000 genomes]
rs743226	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743227	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7493705	1.00[ASN][1000 genomes]
rs8004236	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005261	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8007822	1.00[ASN][1000 genomes]
rs8009666	1.00[ASN][1000 genomes]
rs8010905	1.00[ASN][1000 genomes]
rs8011195	0.85[ASN][1000 genomes]
rs8016140	1.00[ASN][1000 genomes]
rs8019482	0.85[ASN][1000 genomes]
rs8019523	0.85[ASN][1000 genomes]
rs8019700	0.85[ASN][1000 genomes]
rs8019709	0.85[ASN][1000 genomes]
rs876996	1.00[ASN][1000 genomes]
rs9646144	0.93[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	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
5	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
6	nsv1038396	chr14:35714499-35788189	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1045288	chr14:35735886-35788189	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1043840	chr14:35739319-35791879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1794822	chr14:35755087-35761366	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10131625	PPP2R3C	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35716800-35761000	Weak transcription	Spleen	Spleen
2	chr14:35727200-35761000	Weak transcription	NHLF	lung
3	chr14:35737400-35761000	Weak transcription	Gastric	stomach
4	chr14:35744000-35761000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr14:35746000-35761000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:35747200-35761000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:35750600-35761000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr14:35752000-35761000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:35757200-35761000	Weak transcription	Stomach Mucosa	stomach
10	chr14:35759600-35763200	Active TSS	Fetal Kidney	kidney
11	chr14:35760000-35761000	Flanking Active TSS	Dnd41	blood
12	chr14:35760400-35761000	Active TSS	HepG2	liver
13	chr14:35760400-35763400	Active TSS	Placenta	Placenta
14	chr14:35760600-35761000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:35760600-35761000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:35760600-35761000	Enhancers	Fetal Brain Male	brain
17	chr14:35760600-35761400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr14:35760600-35762200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr14:35760600-35762200	Active TSS	Fetal Brain Female	brain
20	chr14:35760600-35762400	Active TSS	Duodenum Mucosa	Duodenum
21	chr14:35760600-35762400	Active TSS	Fetal Stomach	stomach
22	chr14:35760600-35762600	Active TSS	Small Intestine	intestine
23	chr14:35760600-35762800	Active TSS	Right Ventricle	heart
24	chr14:35760600-35763000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:35760600-35763000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:35760600-35763400	Active TSS	Fetal Intestine Small	intestine
27	chr14:35760600-35763600	Active TSS	Fetal Intestine Large	intestine
28	chr14:35760600-35763800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr14:35760600-35765200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:35760800-35761000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:35760800-35761000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:35760800-35761000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:35760800-35761000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr14:35760800-35761000	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr14:35760800-35761000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr14:35760800-35761000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:35760800-35761000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr14:35760800-35761000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr14:35760800-35761000	Flanking Active TSS	Liver	Liver
40	chr14:35760800-35761000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr14:35760800-35761000	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr14:35760800-35761000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr14:35760800-35761000	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr14:35760800-35761000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr14:35760800-35761000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr14:35760800-35761000	Flanking Active TSS	Thymus	Thymus
47	chr14:35760800-35761000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr14:35760800-35761200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr14:35760800-35761200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr14:35760800-35761200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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