Variant report

Variant	rs12461077
Chromosome Location	chr19:36712079-36712080
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36711582..36712244-chr8:25118983..25119572,2	MCF-7	breast:
2	chr19:36703714..36707271-chr19:36711666..36715110,4	MCF-7	breast:
3	chr19:36711072..36713184-chr19:36713372..36715798,2	K562	blood:
4	chr19:36705207..36708225-chr19:36708519..36712657,6	K562	blood:

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction
ENSG00000167635	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10403738	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407835	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407850	0.82[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409983	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412832	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415410	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416509	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416742	0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416925	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419269	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425166	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882933	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459704	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461112	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461855	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462725	0.81[CHB][hapmap]
rs12463157	0.81[AMR][1000 genomes]
rs2271842	0.81[CHB][hapmap]
rs28414272	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528757	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.81[CHB][hapmap]
rs2945955	0.83[CHB][hapmap]
rs3098393	0.82[CHB][hapmap]
rs4361039	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806293	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806294	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806295	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806303	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56206115	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56316708	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56686317	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57385903	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57734651	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295196	0.96[ASN][1000 genomes]
rs61413061	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113093	0.87[EUR][1000 genomes]
rs62113146	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113148	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62113149	0.81[AMR][1000 genomes]
rs62113152	0.81[AMR][1000 genomes]
rs7251745	0.82[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038028	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040107	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040113	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73040148	0.81[AMR][1000 genomes]
rs73041817	0.83[AMR][1000 genomes]
rs8106135	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111860	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12461077	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs12461077	LINC00665	cis	Muscle Skeletal	GTEx
rs12461077	LINC00665	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36706800-36716400	Weak transcription	Aorta	Aorta
2	chr19:36707000-36712800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:36707000-36712800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:36707000-36716200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:36707000-36726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:36707200-36712600	Weak transcription	NHDF-Ad	bronchial
7	chr19:36707400-36730200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:36707600-36712400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:36707600-36712800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:36707600-36713000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:36707800-36712400	Weak transcription	Small Intestine	intestine
13	chr19:36707800-36712800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:36707800-36712800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:36707800-36712800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:36707800-36713000	Weak transcription	Brain Anterior Caudate	brain
17	chr19:36707800-36716400	Weak transcription	Right Ventricle	heart
18	chr19:36707800-36717000	Weak transcription	HSMMtube	muscle
19	chr19:36708000-36712800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:36708000-36712800	Weak transcription	Ovary	ovary
21	chr19:36708000-36713200	Weak transcription	Gastric	stomach
22	chr19:36708000-36714000	Genic enhancers	Dnd41	blood
23	chr19:36708000-36715000	Weak transcription	NHLF	lung
24	chr19:36708000-36716400	Weak transcription	Psoas Muscle	Psoas
25	chr19:36708000-36716800	Weak transcription	Pancreas	Pancrea
26	chr19:36708000-36719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:36708200-36715000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:36708200-36730800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:36708400-36713800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:36708400-36715400	Weak transcription	Fetal Heart	heart
31	chr19:36708400-36716400	Weak transcription	Spleen	Spleen
32	chr19:36708600-36712800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:36708800-36712800	Weak transcription	Right Atrium	heart
34	chr19:36709000-36715400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:36709000-36723000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:36709000-36723800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:36709000-36724000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr19:36709200-36716000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:36709200-36716000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:36709400-36715200	Strong transcription	Fetal Lung	lung
41	chr19:36709400-36723800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:36709600-36713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:36709600-36713200	Strong transcription	Fetal Brain Female	brain
44	chr19:36709800-36714000	Strong transcription	Placenta	Placenta
45	chr19:36710000-36712800	Strong transcription	Left Ventricle	heart
46	chr19:36710000-36713200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr19:36710000-36714000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr19:36710000-36714000	Strong transcription	Osteobl	bone
49	chr19:36710000-36715000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:36710000-36715000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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