Variant report

Variant	rs13042637
Chromosome Location	chr20:13804101-13804102
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	chr20:13802809..13804959-chr20:13816755..13818669,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1018705	0.85[JPT][hapmap]
rs13039364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13039593	0.85[GIH][hapmap];0.88[JPT][hapmap]
rs13042614	0.87[JPT][hapmap]
rs1541059	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1547920	0.93[ASN][1000 genomes]
rs1999112	0.88[CHB][hapmap];0.85[GIH][hapmap];0.88[ASN][1000 genomes]
rs2073290	0.82[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs2209993	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs2209994	0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2327797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2423745	0.88[ASN][1000 genomes]
rs2423749	0.88[CHB][hapmap];0.92[GIH][hapmap];0.91[ASN][1000 genomes]
rs2423750	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs2423753	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3180370	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34449907	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34806363	0.91[ASN][1000 genomes]
rs35361761	0.82[ASN][1000 genomes]
rs35632254	0.82[ASN][1000 genomes]
rs4813139	0.88[CHB][hapmap];0.82[GIH][hapmap]
rs4813142	0.85[ASN][1000 genomes]
rs4814256	0.80[ASN][1000 genomes]
rs4814258	0.88[CHB][hapmap];0.82[GIH][hapmap]
rs6033809	0.88[CHB][hapmap];0.82[GIH][hapmap]
rs6033819	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs6033821	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6042318	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6042319	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6042324	0.88[CHB][hapmap];0.82[GIH][hapmap]
rs6042336	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6042351	0.84[ASN][1000 genomes]
rs6042362	0.88[ASN][1000 genomes]
rs6042425	0.85[GIH][hapmap];0.88[JPT][hapmap]
rs6074637	0.88[CHB][hapmap];0.82[GIH][hapmap]
rs6074643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6074644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6079149	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6079154	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6079156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6079158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6079162	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6079165	0.85[ASN][1000 genomes]
rs6079166	1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs6079176	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6079178	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6079181	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6079182	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6079204	0.88[JPT][hapmap]
rs6110026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6110035	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs6134968	0.84[ASN][1000 genomes]
rs62209178	0.85[ASN][1000 genomes]
rs62209207	0.94[ASN][1000 genomes]
rs68012295	0.93[ASN][1000 genomes]
rs7265467	0.88[CHB][hapmap]
rs754796	0.88[CHB][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13042637	PCSK2	cis	parietal	SCAN
rs13042637	C20orf7	cis	brain	BrainEAC

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13791200-13804800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:13793000-13804200	Weak transcription	Psoas Muscle	Psoas
3	chr20:13793000-13805200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:13795600-13804800	Weak transcription	NHLF	lung
5	chr20:13797400-13804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:13797400-13805000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:13797400-13807000	Weak transcription	Esophagus	oesophagus
8	chr20:13797400-13820200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:13798200-13805000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr20:13798600-13804200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr20:13798800-13804200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr20:13798800-13804600	Weak transcription	Right Ventricle	heart
13	chr20:13799000-13804800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:13799400-13804200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr20:13799400-13804600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:13799400-13805000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:13799400-13805200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr20:13799400-13805400	Weak transcription	Primary T cells from cord blood	blood
19	chr20:13799400-13807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr20:13799600-13804600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr20:13799600-13804800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr20:13799600-13804800	Weak transcription	HepG2	liver
23	chr20:13799600-13805000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr20:13799600-13807000	Weak transcription	Left Ventricle	heart
25	chr20:13799600-13808000	Weak transcription	Brain Hippocampus Middle	brain
26	chr20:13799800-13804400	Weak transcription	Fetal Intestine Large	intestine
27	chr20:13799800-13807800	Weak transcription	Brain Anterior Caudate	brain
28	chr20:13801000-13804200	Weak transcription	Fetal Muscle Leg	muscle
29	chr20:13802000-13804800	Weak transcription	Dnd41	blood
30	chr20:13802200-13804400	Weak transcription	HSMMtube	muscle
31	chr20:13803000-13805800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr20:13803200-13804800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr20:13804000-13804600	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links