Variant report

Variant	rs930665
Chromosome Location	chr12:122245831-122245832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:122245570-122245840	GM12878	blood:	n/a	chr12:122245760-122245773 chr12:122245727-122245734
2	POLR2A	chr12:122245489-122246802	K562	blood:	n/a	n/a
3	POLR2A	chr12:122245570-122246390	K562	blood:	n/a	n/a
4	SPI1	chr12:122245460-122246008	HL-60	blood:	n/a	chr12:122245760-122245773 chr12:122245727-122245734

No.	Distal block	Cell Line	Cell type
1	chr12:122244343..122246026-chr12:122447313..122449275,2	K562	blood:
2	chr12:122245726..122247591-chr9:117348115..117350382,2	MCF-7	breast:
3	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
4	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212694	TF binding region
RHOF	TF binding region
ENSG00000256950	Chromatin interaction
ENSG00000136888	Chromatin interaction
ENSG00000110801	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1004390	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11043202	0.93[EUR][1000 genomes]
rs11043203	0.93[EUR][1000 genomes]
rs11043207	0.84[EUR][1000 genomes]
rs1168663	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168664	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168665	0.89[EUR][1000 genomes]
rs1168666	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168668	0.90[EUR][1000 genomes]
rs1168669	0.93[EUR][1000 genomes]
rs1168671	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168672	0.93[EUR][1000 genomes]
rs1168673	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12307227	0.92[EUR][1000 genomes]
rs12823194	0.81[EUR][1000 genomes]
rs1667578	0.93[EUR][1000 genomes]
rs1667579	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795965	0.94[EUR][1000 genomes]
rs1795966	0.81[EUR][1000 genomes]
rs2019561	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2019562	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122266	0.92[EUR][1000 genomes]
rs2707066	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2707067	0.90[EUR][1000 genomes]
rs712852	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957564	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974348	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895951	0.93[EUR][1000 genomes]
rs895952	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs895953	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs895954	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895957	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs921286	0.92[EUR][1000 genomes]
rs921287	0.85[AMR][1000 genomes];0.95[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs930665	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122241600-122248600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:122243800-122246800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:122243800-122251600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122244000-122246200	Genic enhancers	Spleen	Spleen
5	chr12:122244400-122249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122244600-122246000	Genic enhancers	Lung	lung
7	chr12:122244600-122246400	Genic enhancers	Placenta	Placenta
8	chr12:122244600-122246600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122244600-122246600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:122244800-122246000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
11	chr12:122244800-122246400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:122244800-122249200	Weak transcription	Psoas Muscle	Psoas
13	chr12:122245000-122246000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr12:122245000-122246000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:122245000-122246000	Weak transcription	Aorta	Aorta
16	chr12:122245000-122246000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr12:122245000-122246000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr12:122245000-122246200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:122245000-122246200	Genic enhancers	Primary hematopoietic stem cells	blood
20	chr12:122245000-122246200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:122245000-122246200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:122245000-122246200	Genic enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:122245000-122246400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:122245000-122246400	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:122245000-122246400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:122245000-122246400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:122245000-122246400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr12:122245000-122246400	Weak transcription	HMEC	breast
29	chr12:122245000-122246600	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr12:122245000-122246600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:122245000-122248800	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr12:122245000-122248800	Weak transcription	Fetal Kidney	kidney
33	chr12:122245200-122246000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:122245200-122246000	Enhancers	Primary T cells from cord blood	blood
35	chr12:122245200-122246000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr12:122245200-122246000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr12:122245200-122246000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:122245200-122246000	Enhancers	Liver	Liver
39	chr12:122245200-122246000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:122245200-122246000	Weak transcription	Ovary	ovary
41	chr12:122245200-122246200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:122245200-122246200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:122245200-122246200	Genic enhancers	Fetal Intestine Small	intestine
44	chr12:122245200-122246200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:122245200-122246400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:122245200-122246400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:122245200-122246400	Weak transcription	Brain Angular Gyrus	brain
48	chr12:122245200-122246400	Genic enhancers	Stomach Smooth Muscle	stomach
49	chr12:122245200-122246400	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr12:122245200-122246600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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