Variant report

Variant	rs12408242
Chromosome Location	chr1:160061934-160061935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160056237..160058105-chr1:160061852..160063937,2	K562	blood:
2	chr1:160061469..160063208-chr1:160229753..160232455,2	K562	blood:

Variant related genes	Relation type
ENSG00000228606	Chromatin interaction
ENSG00000132716	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1131891	0.87[CEU][hapmap]
rs12092798	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12401728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402888	0.87[CEU][hapmap]
rs2295621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295622	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747619	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12408242	IGSF8	cis	parietal	SCAN
rs12408242	KCNN3	cis	cerebellum	SCAN
rs12408242	ZBTB7B	cis	cerebellum	SCAN
rs12408242	LY9	cis	cerebellum	SCAN
rs12408242	PEX19	cis	parietal	SCAN
rs12408242	CASQ1	cis	parietal	SCAN
rs12408242	SMG5	cis	parietal	SCAN
rs12408242	IGSF8	cis	cerebellum	SCAN
rs12408242	CD1B	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160053000-160065200	Weak transcription	Hela-S3	cervix
2	chr1:160053200-160062000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:160053600-160063200	Weak transcription	Small Intestine	intestine
4	chr1:160053800-160066000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:160054000-160066400	Weak transcription	NHDF-Ad	bronchial
6	chr1:160054200-160063400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:160054400-160064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:160054400-160065400	Weak transcription	Right Atrium	heart
9	chr1:160054400-160066000	Weak transcription	GM12878-XiMat	blood
10	chr1:160054400-160066200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:160054400-160066200	Weak transcription	HMEC	breast
12	chr1:160054400-160066600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:160054600-160063000	Strong transcription	Thymus	Thymus
14	chr1:160054800-160062000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:160055800-160063000	Strong transcription	Fetal Intestine Small	intestine
16	chr1:160055800-160065400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:160055800-160066400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:160056000-160065400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:160056400-160063000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:160056400-160065200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:160056600-160062400	Strong transcription	Liver	Liver
22	chr1:160056600-160063000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:160056600-160063200	Strong transcription	Primary T cells from cord blood	blood
24	chr1:160056600-160065400	Genic enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:160056800-160065200	Strong transcription	Adipose Nuclei	Adipose
26	chr1:160056800-160065600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:160056800-160066400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:160057000-160063000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:160057000-160063400	Strong transcription	Fetal Stomach	stomach
30	chr1:160057000-160063400	Strong transcription	Spleen	Spleen
31	chr1:160057000-160064400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr1:160057000-160064800	Strong transcription	Ovary	ovary
33	chr1:160057000-160065000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:160057000-160065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:160057200-160065000	Strong transcription	Lung	lung
36	chr1:160057200-160065400	Weak transcription	Fetal Brain Male	brain
37	chr1:160057400-160065200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:160057600-160062200	Strong transcription	Primary B cells from cord blood	blood
39	chr1:160057600-160063400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:160057600-160063600	Genic enhancers	Brain Hippocampus Middle	brain
41	chr1:160057600-160066400	Weak transcription	HSMM	muscle
42	chr1:160057800-160065200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:160057800-160065400	Strong transcription	Brain Germinal Matrix	brain
44	chr1:160057800-160065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:160058000-160062600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:160058000-160063000	Strong transcription	Fetal Thymus	thymus
47	chr1:160058000-160063200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:160058000-160064800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:160058000-160065200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:160058200-160062800	Strong transcription	Fetal Intestine Large	intestine

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