Variant report

Variant	rs1060186
Chromosome Location	chr19:39221295-39221296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39215761..39217531-chr19:39221029..39224006,3	MCF-7	breast:
2	chr19:39219983..39221932-chr19:39339687..39341437,2	K562	blood:
3	chr19:39151862..39154243-chr19:39220891..39223454,2	MCF-7	breast:
4	chr19:39219110..39222682-chr19:39328590..39331481,3	MCF-7	breast:
5	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
6	chr19:39219113..39222952-chr19:39339497..39343491,5	K562	blood:
7	chr19:39218752..39222924-chr19:39336082..39338597,4	K562	blood:
8	chr19:39219453..39221729-chr19:39388721..39391433,2	K562	blood:
9	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
10	chr19:39220085..39221699-chr19:39321013..39323268,2	MCF-7	breast:
11	chr19:39210151..39212274-chr19:39220710..39223551,2	MCF-7	breast:
12	chr19:39173021..39174655-chr19:39220588..39222676,2	MCF-7	breast:
13	chr19:39217938..39222423-chr19:39330106..39333750,7	K562	blood:
14	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
15	chr19:39221109..39222867-chr19:39294750..39296802,2	MCF-7	breast:
16	chr19:39138000..39140768-chr19:39215687..39223350,9	MCF-7	breast:
17	chr19:39218316..39221729-chr19:39388696..39391433,3	K562	blood:
18	chr19:39220355..39222395-chr19:39320677..39322335,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269688	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1031849	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10421863	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.95[AMR][1000 genomes]
rs10424568	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11083476	0.92[AMR][1000 genomes]
rs11665964	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11672576	0.95[AMR][1000 genomes]
rs12462503	0.83[ASW][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12984247	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1564203	0.83[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2080988	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2112649	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786841	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3786843	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4347742	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4619518	0.95[AMR][1000 genomes]
rs4801861	0.89[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802743	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6508813	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs6508814	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7249585	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7252630	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs749701	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs752067	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs8099948	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107877	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs888997	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9304576	0.89[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap]
rs9304577	0.94[JPT][hapmap]
rs936524	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1060186	RPS16	cis	parietal	SCAN
rs1060186	CAPN12	cis	multi-tissue	Pritchard
rs1060186	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs1060186	C19orf54	cis	parietal	SCAN
rs1060186	SFRS16	cis	parietal	SCAN
rs1060186	ERF	cis	cerebellum	SCAN
rs1060186	CAPN12	cis	Adipose Subcutaneous	GTEx
rs1060186	LGALS17A	cis	cerebellum	SCAN
rs1060186	CAPN12	cis	lymphoblastoid	seeQTL
rs1060186	CAPN12	cis	Heart Left Ventricle	GTEx
rs1060186	CAPN12	cis	Esophagus Muscularis	GTEx
rs1060186	PPP1R13L	cis	cerebellum	SCAN
rs1060186	MEGF8	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:39190400-39222600	Strong transcription	Dnd41	blood
8	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr19:39202800-39221400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr19:39204200-39223400	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr19:39207000-39222400	Strong transcription	Fetal Brain Female	brain
19	chr19:39210200-39222600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:39210400-39223400	Strong transcription	NHLF	lung
21	chr19:39210400-39223400	Strong transcription	Osteobl	bone
22	chr19:39210600-39222000	Strong transcription	Small Intestine	intestine
23	chr19:39210600-39222800	Genic enhancers	Spleen	Spleen
24	chr19:39211200-39221400	Strong transcription	Esophagus	oesophagus
25	chr19:39211200-39222000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:39211200-39224000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:39211600-39223000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:39212600-39222800	Strong transcription	Aorta	Aorta
29	chr19:39213000-39221800	Strong transcription	HMEC	breast
30	chr19:39213000-39223400	Strong transcription	Brain Germinal Matrix	brain
31	chr19:39213200-39223600	Strong transcription	HSMMtube	muscle
32	chr19:39213400-39222200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:39213400-39222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:39213400-39223200	Strong transcription	Fetal Stomach	stomach
35	chr19:39213400-39223600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:39213400-39224400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:39213800-39223600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:39213800-39224400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:39214000-39224800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:39214400-39222800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39214400-39224000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:39214800-39222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:39215600-39224000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:39215600-39224800	Genic enhancers	A549	lung
45	chr19:39216200-39223800	Weak transcription	Fetal Thymus	thymus
46	chr19:39217000-39224400	Genic enhancers	Fetal Intestine Large	intestine
47	chr19:39217200-39224400	Genic enhancers	Fetal Intestine Small	intestine
48	chr19:39217800-39222800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:39217800-39224200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr19:39217800-39224200	Weak transcription	GM12878-XiMat	blood

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