Variant report

Variant	rs4142285
Chromosome Location	chr13:50054308-50054309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1409016	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1536194	0.81[EUR][1000 genomes]
rs1543514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555530	0.86[EUR][1000 genomes]
rs1812	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1853324	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2031532	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs2057413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057415	0.86[EUR][1000 genomes]
rs2057417	0.86[EUR][1000 genomes]
rs2407692	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407693	0.91[ASN][1000 genomes]
rs3764090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3764091	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4417458	0.87[ASN][1000 genomes]
rs4941642	0.80[EUR][1000 genomes]
rs4942835	0.84[ASN][1000 genomes]
rs6561525	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561527	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561528	0.91[ASN][1000 genomes]
rs6561529	0.91[ASN][1000 genomes]
rs7139634	0.83[EUR][1000 genomes]
rs7321228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321670	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7324622	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7328782	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330512	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7337488	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7982297	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7982598	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7987293	0.81[EUR][1000 genomes]
rs7992603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994115	0.81[EUR][1000 genomes]
rs7996852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998022	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7998427	0.81[EUR][1000 genomes]
rs7998660	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8000149	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9316453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526564	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535241	0.89[JPT][hapmap]
rs9535243	0.84[EUR][1000 genomes]
rs9535249	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9568219	0.86[EUR][1000 genomes]
rs959421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967163	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs967164	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription 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	27 gene(s)	inside rSNPs	diseases
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4142285	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs4142285	CAB39L	cis	cerebellum	SCAN
rs4142285	RNASEH2B	cis	parietal	SCAN
rs4142285	RB1	cis	cerebellum	SCAN
rs4142285	SETDB2	cis	parietal	SCAN
rs4142285	SETDB2	cis	cerebellum	SCAN
rs4142285	ARL11	cis	parietal	SCAN
rs4142285	EBPL	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50020200-50068400	Weak transcription	HMEC	breast
2	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
3	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
4	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
5	chr13:50034400-50068800	Weak transcription	NH-A	brain
6	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
7	chr13:50036600-50068000	Weak transcription	K562	blood
8	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
10	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
11	chr13:50038000-50062800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr13:50038000-50063400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr13:50038000-50063600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:50038000-50063800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:50038200-50062400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:50038200-50063400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr13:50038400-50062200	Strong transcription	Primary T cells from cord blood	blood
19	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
23	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:50038800-50069000	Weak transcription	HSMM	muscle
25	chr13:50039000-50068200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:50040600-50064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:50041400-50056000	Strong transcription	Primary B cells from cord blood	blood
31	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:50041600-50063800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:50042000-50063400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr13:50042200-50067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr13:50042800-50056400	Strong transcription	Fetal Thymus	thymus
36	chr13:50044000-50054600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr13:50044400-50056600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:50045800-50056200	Strong transcription	GM12878-XiMat	blood
39	chr13:50047000-50056200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:50047400-50063400	Strong transcription	Liver	Liver
41	chr13:50047600-50063600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:50047800-50055200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:50048200-50056200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:50048200-50056400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:50048400-50055200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:50048400-50055400	Strong transcription	Adipose Nuclei	Adipose
47	chr13:50048600-50054400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:50048600-50055400	Strong transcription	HepG2	liver
49	chr13:50048600-50056200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr13:50048600-50057200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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