Variant report

Variant	rs12046199
Chromosome Location	chr1:86844127-86844128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11161808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12022446	0.83[AMR][1000 genomes]
rs12023726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023799	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12029568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12030666	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12032435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12037391	0.83[AMR][1000 genomes]
rs12038144	0.83[AMR][1000 genomes]
rs12038844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12039899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042822	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12043873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12044970	0.83[AMR][1000 genomes]
rs12045012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045465	0.83[AMR][1000 genomes]
rs12046894	0.83[AMR][1000 genomes]
rs12047304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12047305	0.94[ASN][1000 genomes]
rs12047913	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12048082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12747430	0.83[ASN][1000 genomes]
rs2274999	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28688345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28788025	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34204564	0.95[ASN][1000 genomes]
rs3737671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3765509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820038	0.83[AMR][1000 genomes]
rs4497186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55857117	0.83[ASN][1000 genomes]
rs57955693	0.83[ASN][1000 genomes]
rs58658794	0.83[ASN][1000 genomes]
rs59775624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS 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 miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription 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 miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
2	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
5	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
6	chr1:86820400-86846200	Weak transcription	NHLF	lung
7	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:86820400-86847000	Weak transcription	Liver	Liver
9	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:86820400-86860200	Weak transcription	NHEK	skin
11	chr1:86820600-86848000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:86822400-86846200	Weak transcription	Gastric	stomach
13	chr1:86824000-86848200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
15	chr1:86838200-86845800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:86839800-86846800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:86839800-86848200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:86840600-86848200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:86840600-86859600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:86840800-86848600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:86841000-86849000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:86841000-86849400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:86841000-86851400	Weak transcription	HMEC	breast
24	chr1:86841000-86854400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:86841000-86859800	Weak transcription	HSMM	muscle
26	chr1:86841600-86845800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:86841600-86859800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:86841800-86855000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:86842000-86845000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:86842000-86845000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:86842000-86846200	Weak transcription	NHDF-Ad	bronchial
32	chr1:86842200-86844400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:86842200-86845000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:86842200-86847000	Weak transcription	HUVEC	blood vessel
35	chr1:86842400-86844400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:86842400-86844400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr1:86842400-86844400	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr1:86842400-86845000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:86842400-86848200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:86842600-86844200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr1:86842600-86844400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr1:86842600-86844600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:86842600-86844800	Strong transcription	Primary T cells from cord blood	blood
44	chr1:86842600-86844800	ZNF genes & repeats	Brain Germinal Matrix	brain
45	chr1:86842600-86845000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:86842800-86844200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr1:86842800-86844800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
48	chr1:86842800-86845000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:86842800-86845000	ZNF genes & repeats	Dnd41	blood
50	chr1:86843400-86844400	Strong transcription	Fetal Lung	lung

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