Variant report

Variant	rs12609505
Chromosome Location	chr19:18674057-18674058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18667740..18670829-chr19:18672165..18676171,4	K562	blood:
2	chr19:18667302..18670613-chr19:18674047..18675732,3	MCF-7	breast:
3	chr19:18672789..18675551-chr19:18697478..18700004,2	MCF-7	breast:
4	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:

Variant related genes	Relation type
ENSG00000221983	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000268983	Chromatin interaction
ENSG00000105700	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10402321	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10409392	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs10414427	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10425018	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1043192	0.81[JPT][hapmap]
rs11086114	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086116	0.85[ASN][1000 genomes]
rs11667551	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11672297	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12150991	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12608925	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1862645	0.81[JPT][hapmap]
rs2057649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058077	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079015	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2079016	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2238650	0.81[JPT][hapmap]
rs2283616	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302055	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2314664	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2314665	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2314666	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2314667	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28451415	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28711754	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28884574	0.80[ASN][1000 genomes]
rs3170474	0.85[JPT][hapmap]
rs35867875	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35875334	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36050418	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3761032	0.81[JPT][hapmap]
rs3761034	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3761036	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803917	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4629093	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808821	0.85[ASN][1000 genomes]
rs4808839	0.81[JPT][hapmap]
rs55724121	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55888366	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58782998	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59798925	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137086	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137090	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6554	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709679	0.81[JPT][hapmap]
rs7247557	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7250192	0.81[JPT][hapmap]
rs7250623	0.90[JPT][hapmap]
rs7253088	0.87[ASN][1000 genomes]
rs7254004	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256319	0.85[JPT][hapmap]
rs7258480	0.82[ASN][1000 genomes]
rs7648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109364	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs8110371	0.83[ASN][1000 genomes]
rs8110374	0.83[ASN][1000 genomes]
rs916791	0.81[JPT][hapmap]

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	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv911284	chr19:18643036-18684216	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12609505	NDUFA13	cis	parietal	SCAN
rs12609505	UBA52	Cis_1M	lymphoblastoid	RTeQTL
rs12609505	UBA52	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18669400-18675600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:18669600-18674800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:18669600-18675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:18669600-18675400	Weak transcription	Fetal Kidney	kidney
5	chr19:18669600-18677600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:18669800-18674200	Weak transcription	Esophagus	oesophagus
7	chr19:18669800-18674600	Weak transcription	Small Intestine	intestine
8	chr19:18669800-18675400	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:18669800-18682000	Weak transcription	Fetal Brain Male	brain
10	chr19:18669800-18682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:18670200-18675400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:18670200-18681200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18670400-18675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:18670400-18675400	Weak transcription	Stomach Mucosa	stomach
15	chr19:18670600-18675400	Weak transcription	Primary B cells from cord blood	blood
16	chr19:18670600-18675400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:18670600-18675400	Weak transcription	HMEC	breast
18	chr19:18670600-18675400	Weak transcription	HSMMtube	muscle
19	chr19:18670600-18675400	Weak transcription	K562	blood
20	chr19:18670600-18675400	Weak transcription	NHDF-Ad	bronchial
21	chr19:18670600-18675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:18670600-18677800	Weak transcription	Psoas Muscle	Psoas
23	chr19:18670600-18678000	Weak transcription	A549	lung
24	chr19:18670600-18678400	Weak transcription	Hela-S3	cervix
25	chr19:18670600-18681200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:18670600-18682000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:18671000-18681200	Strong transcription	Fetal Intestine Small	intestine
28	chr19:18671000-18681200	Strong transcription	Fetal Stomach	stomach
29	chr19:18671000-18681400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:18671200-18680600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:18671200-18680600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:18671200-18680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:18671200-18680600	Strong transcription	Fetal Brain Female	brain
34	chr19:18671200-18680600	Strong transcription	Fetal Intestine Large	intestine
35	chr19:18671200-18680600	Strong transcription	Fetal Thymus	thymus
36	chr19:18671200-18681200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:18671200-18681200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:18671400-18681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:18671800-18674400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:18671800-18674400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:18671800-18680200	Strong transcription	Brain Hippocampus Middle	brain
42	chr19:18671800-18680600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:18671800-18680600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:18672200-18680600	Strong transcription	Brain Germinal Matrix	brain
45	chr19:18672400-18674200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:18672400-18674400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:18672400-18674400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:18672400-18674400	Genic enhancers	Placenta	Placenta
49	chr19:18672400-18674400	Strong transcription	HepG2	liver
50	chr19:18672400-18676000	Strong transcription	Brain Angular Gyrus	brain

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