Variant report

Variant	rs2526875
Chromosome Location	chr14:71378360-71378361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71376693..71378500-chr14:71379508..71383597,4	MCF-7	breast:
2	chr14:71372925..71376620-chr14:71377787..71383660,12	MCF-7	breast:
3	chr14:71376408..71378571-chr14:71380621..71383425,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10132789	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10132984	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10140225	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10140917	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10145824	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10148324	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10150408	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs116016	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11623266	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12893492	0.80[EUR][1000 genomes]
rs12896829	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1468470	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1558097	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1978164	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2010713	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2097975	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240341	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240531	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2251394	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286311	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2332506	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526847	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526848	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526856	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526859	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526864	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526867	1.00[CHB][hapmap]
rs2526871	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526873	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526880	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526881	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526883	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526884	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526887	0.81[ASN][1000 genomes]
rs2810072	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810074	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810077	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2810078	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810079	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2810081	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2810082	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs2810101	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810109	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810111	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2810113	1.00[CHB][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2810118	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2877708	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2877714	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3784067	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4132848	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4147077	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366661	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4467005	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4531677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4899382	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs58938327	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6573994	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7143595	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap]
rs714421	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7144986	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7145285	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7147862	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7150037	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7151145	0.92[ASN][1000 genomes]
rs7152845	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7154437	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7155247	0.94[JPT][hapmap]
rs7156009	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs7160958	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8004452	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8005160	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8006046	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs8007425	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8008111	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs8020480	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8021824	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs917067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323556	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9323557	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers 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	35 gene(s)	inside rSNPs	diseases
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1039769	chr14:71310954-71525720	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv542128	chr14:71310954-71525720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1053303	chr14:71316325-71402971	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2526875	PCNX	cis	Thyroid	GTEx
rs2526875	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2526875	PCNX	cis	Artery Aorta	GTEx
rs2526875	PCNX	cis	Artery Tibial	GTEx
rs2526875	PCNX	cis	Nerve Tibial	GTEx
rs2526875	PCNX	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71375600-71398400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:71376000-71379200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:71376000-71379400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr14:71376000-71380800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:71376000-71396800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:71376000-71401000	Weak transcription	Lung	lung
7	chr14:71376200-71379200	Weak transcription	Aorta	Aorta
8	chr14:71376200-71379600	Enhancers	Liver	Liver
9	chr14:71376200-71380200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr14:71376200-71383000	Weak transcription	Fetal Muscle Leg	muscle
11	chr14:71376400-71378600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:71376400-71378600	Enhancers	Adipose Nuclei	Adipose
13	chr14:71376400-71379000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr14:71376400-71379400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr14:71376400-71380200	Enhancers	HepG2	liver
16	chr14:71376400-71381000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr14:71376600-71378400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:71376600-71378600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr14:71376600-71379200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:71376600-71379400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:71376600-71380000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr14:71376600-71380000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr14:71376600-71380400	Enhancers	Fetal Intestine Large	intestine
24	chr14:71376600-71381000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr14:71376600-71385400	Weak transcription	HUVEC	blood vessel
26	chr14:71376600-71386000	Weak transcription	Fetal Lung	lung
27	chr14:71376600-71389000	Weak transcription	HSMMtube	muscle
28	chr14:71376600-71398400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr14:71376800-71380000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:71376800-71386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:71377000-71378400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr14:71377000-71378600	Enhancers	Fetal Intestine Small	intestine
33	chr14:71377000-71383600	Weak transcription	HSMM	muscle
34	chr14:71377200-71378400	Enhancers	NHEK	skin
35	chr14:71377200-71380000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:71377200-71380400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:71377200-71384400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr14:71377200-71386600	Weak transcription	NHDF-Ad	bronchial
39	chr14:71377400-71378400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:71377400-71378600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr14:71377400-71378600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:71377400-71378600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr14:71377400-71379200	Weak transcription	Primary T cells from cord blood	blood
44	chr14:71377400-71379200	Weak transcription	Left Ventricle	heart
45	chr14:71377400-71379200	Weak transcription	Ovary	ovary
46	chr14:71377400-71379400	Weak transcription	Psoas Muscle	Psoas
47	chr14:71377400-71379800	Weak transcription	Spleen	Spleen
48	chr14:71377400-71381000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:71377400-71381800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:71377400-71382200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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