Variant report

Variant	rs589332
Chromosome Location	chr1:85412436-85412437
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	chr1:85411165..85413303-chr1:85416818..85418943,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12064092	0.86[YRI][hapmap]
rs12118848	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs12120635	0.89[CEU][hapmap]
rs12145036	0.83[GIH][hapmap]
rs12402639	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12402681	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1325277	0.82[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55873701	0.85[EUR][1000 genomes]
rs570564	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs621003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639500	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs650357	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666779	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs589332	CLCA4	cis	cerebellum	SCAN
rs589332	DDAH1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85405000-85413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:85405200-85413000	Weak transcription	Esophagus	oesophagus
4	chr1:85410400-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:85410600-85412600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:85410600-85413400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:85410800-85412600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:85410800-85413200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:85411200-85413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:85411200-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:85411200-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:85411200-85414200	Enhancers	NHEK	skin
13	chr1:85411200-85414600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:85411400-85412600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:85411400-85412600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:85411400-85412600	Enhancers	A549	lung
17	chr1:85411400-85412600	Enhancers	NH-A	brain
18	chr1:85411400-85412600	Enhancers	NHLF	lung
19	chr1:85411400-85412800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:85411400-85412800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:85411400-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:85411400-85416400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:85411400-85426200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:85411600-85414400	Genic enhancers	GM12878-XiMat	blood
25	chr1:85411800-85412600	Enhancers	NHDF-Ad	bronchial
26	chr1:85411800-85413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:85411800-85416200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:85412000-85412800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:85412000-85413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:85412000-85413000	Weak transcription	Dnd41	blood
31	chr1:85412000-85413000	Weak transcription	HMEC	breast
32	chr1:85412000-85413200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:85412000-85415200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:85412000-85415600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:85412000-85424600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:85412000-85425200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:85412200-85413000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:85412200-85413200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr1:85412200-85415400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:85412200-85430200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:85412400-85412800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:85412400-85413000	Weak transcription	H1 Cell Line	embryonic stem cell

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