Variant report

Variant	rs12050042
Chromosome Location	chr13:50071707-50071708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50071647..50073472-chr13:50180377..50183221,3	MCF-7	breast:
2	chr13:50016481..50018378-chr13:50070335..50072171,3	K562	blood:
3	chr13:50016483..50020444-chr13:50068529..50072853,4	MCF-7	breast:
4	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
5	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000236577	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1409016	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs1536194	0.97[ASN][1000 genomes]
rs1555530	0.97[ASN][1000 genomes]
rs1812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs1980794	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980795	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998782	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2057415	0.94[ASN][1000 genomes]
rs2057417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2407689	0.92[ASN][1000 genomes]
rs3764085	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4468500	0.90[ASN][1000 genomes]
rs4941642	0.94[ASN][1000 genomes]
rs4942831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4942832	0.91[ASN][1000 genomes]
rs6561527	0.83[EUR][1000 genomes]
rs71188363	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139634	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721458	0.92[ASN][1000 genomes]
rs7324622	0.83[EUR][1000 genomes]
rs7329078	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7337488	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs7338755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7987293	0.97[ASN][1000 genomes]
rs7994115	0.97[ASN][1000 genomes]
rs7994130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7998427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs9526569	0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs9535248	0.92[ASN][1000 genomes]
rs9535249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9568219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9568223	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967163	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs967164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12050042	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs12050042	SETDB2	cis	parietal	SCAN
rs12050042	ST13P4	cis	cerebellum	SCAN
rs12050042	SETDB2	cis	cerebellum	SCAN
rs12050042	LPAR6	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50069000-50071800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr13:50069200-50071800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
4	chr13:50070400-50072200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:50070600-50073400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:50070800-50072600	Weak transcription	Liver	Liver
7	chr13:50070800-50072800	Weak transcription	Fetal Intestine Large	intestine
8	chr13:50070800-50073600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:50070800-50073600	Weak transcription	HMEC	breast
10	chr13:50070800-50074200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:50070800-50074400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:50070800-50074400	Weak transcription	Small Intestine	intestine
13	chr13:50070800-50074800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:50070800-50076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:50070800-50076200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:50070800-50076400	Weak transcription	Fetal Lung	lung
17	chr13:50070800-50076800	Weak transcription	Left Ventricle	heart
18	chr13:50070800-50077000	Weak transcription	Gastric	stomach
19	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
20	chr13:50070800-50086800	Weak transcription	Ovary	ovary
21	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
22	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
24	chr13:50070800-50087800	Weak transcription	NHEK	skin
25	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
27	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
28	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
31	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
32	chr13:50071000-50071800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr13:50071000-50071800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:50071000-50071800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:50071000-50071800	Enhancers	Pancreas	Pancrea
36	chr13:50071000-50072000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr13:50071000-50072000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr13:50071000-50072200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr13:50071000-50072200	Enhancers	Spleen	Spleen
40	chr13:50071000-50072400	Enhancers	Primary B cells from peripheral blood	blood
41	chr13:50071000-50072400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr13:50071000-50072600	Weak transcription	NHDF-Ad	bronchial
43	chr13:50071000-50072800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:50071000-50072800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:50071000-50072800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr13:50071000-50072800	Weak transcription	Fetal Heart	heart
47	chr13:50071000-50072800	Weak transcription	NHLF	lung
48	chr13:50071000-50073000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:50071000-50073000	Weak transcription	Primary T cells from cord blood	blood
50	chr13:50071000-50073000	Weak transcription	Osteobl	bone

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