Variant report

Variant	rs12077004
Chromosome Location	chr1:161158348-161158349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161157327..161160707-chr1:161160939..161164830,4	K562	blood:
2	chr1:161151959..161155347-chr1:161155408..161158666,4	K562	blood:
3	chr1:161155867..161158709-chr1:161165222..161166749,2	K562	blood:
4	chr1:161139949..161143125-chr1:161156905..161159223,3	K562	blood:
5	chr1:161136515..161138219-chr1:161157715..161160572,2	K562	blood:
6	chr1:161154836..161159906-chr1:161168588..161174016,8	K562	blood:

Variant related genes	Relation type
ENSG00000158864	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000158859	Chromatin interaction
ENSG00000143224	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1128752	1.00[JPT][hapmap]
rs11576415	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11583589	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12027719	1.00[JPT][hapmap]
rs12094497	1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2301288	1.00[JPT][hapmap]
rs3402	1.00[ASW][hapmap]
rs34448954	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6413453	1.00[ASW][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12077004	OR6Y1	cis	cerebellum	SCAN
rs12077004	CRABP2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161147800-161160600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:161147800-161167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:161148200-161160400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:161148200-161160400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:161148200-161161000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:161148200-161162400	Weak transcription	Liver	Liver
7	chr1:161148200-161162600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:161148200-161167400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:161148400-161161200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:161148400-161165000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:161150600-161158400	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:161150600-161159400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:161150600-161162000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:161152000-161158600	Enhancers	Fetal Thymus	thymus
15	chr1:161153200-161160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:161153200-161166000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:161153200-161167000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:161153800-161159400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:161154000-161160800	Weak transcription	Ovary	ovary
20	chr1:161154000-161161000	Weak transcription	Gastric	stomach
21	chr1:161154200-161158800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:161154400-161159600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:161154600-161159600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:161154800-161159800	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:161155200-161158600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:161155200-161158800	Enhancers	Placenta	Placenta
27	chr1:161155200-161160400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:161155400-161161000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:161155600-161158400	Enhancers	Spleen	Spleen
30	chr1:161155600-161159800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:161155600-161160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:161155800-161158600	Enhancers	Primary B cells from cord blood	blood
33	chr1:161155800-161159600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:161155800-161159600	Weak transcription	Fetal Stomach	stomach
35	chr1:161155800-161159800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:161155800-161160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:161155800-161160400	Weak transcription	NHLF	lung
38	chr1:161156000-161158800	Enhancers	Primary T cells from cord blood	blood
39	chr1:161156000-161159000	Weak transcription	Osteobl	bone
40	chr1:161156000-161159200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:161156000-161161000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:161156000-161162400	Weak transcription	Brain Germinal Matrix	brain
43	chr1:161156000-161167600	Weak transcription	Fetal Heart	heart
44	chr1:161156200-161158400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:161156200-161159200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:161156200-161159400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:161156200-161159600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:161156200-161159600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:161156200-161159800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:161156200-161160600	Weak transcription	Fetal Intestine Small	intestine

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