Variant report

Variant	rs1340981
Chromosome Location	chr1:161711252-161711253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161456869..161457835-chr1:161710956..161711879,5	K562	blood:
2	chr1:161449421..161451787-chr1:161709912..161712102,2	K562	blood:
3	chr1:161617105..161617670-chr1:161711057..161711617,2	MCF-7	breast:
4	chr1:161454518..161455083-chr1:161710546..161711492,2	K562	blood:
5	chr1:161709954..161712481-chr1:161715478..161718294,2	MCF-7	breast:
6	chr1:161616209..161618831-chr1:161708579..161712751,3	MCF-7	breast:
7	chr1:161708205..161716175-chr1:161716206..161720292,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1027701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063178	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs10917821	0.81[EUR][1000 genomes]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12121310	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs12121500	0.93[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12121522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564653	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12745240	0.81[GIH][hapmap]
rs1417580	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1417581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2066247	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs2174208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657096	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657097	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657098	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427626	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7540096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv1005615	chr1:161707312-161714444	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1340981	PEAR1	cis	parietal	SCAN
rs1340981	PEAR1	cis	cerebellum	SCAN
rs1340981	C1orf61	cis	cerebellum	SCAN
rs1340981	ETV3L	cis	cerebellum	SCAN
rs1340981	KCNJ9	cis	parietal	SCAN
rs1340981	ARHGEF11	cis	cerebellum	SCAN
rs1340981	SLAMF7	cis	parietal	SCAN
rs1340981	DUSP12	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161704000-161713800	Weak transcription	HUVEC	blood vessel
2	chr1:161706800-161713600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:161706800-161718800	Weak transcription	NH-A	brain
4	chr1:161707000-161711600	Enhancers	K562	blood
5	chr1:161707200-161711400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:161707400-161713000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:161707600-161713000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:161707600-161713200	Weak transcription	NHDF-Ad	bronchial
9	chr1:161707600-161719200	Weak transcription	NHLF	lung
10	chr1:161707800-161711600	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:161708200-161711400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:161708200-161711400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:161708200-161711600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:161708200-161713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:161708400-161711400	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:161708400-161711400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:161708400-161711400	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:161708600-161711400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:161708800-161711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:161709200-161711400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:161709200-161713000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:161709400-161711400	Enhancers	Adipose Nuclei	Adipose
23	chr1:161709600-161711400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:161709600-161711400	Enhancers	Liver	Liver
25	chr1:161710400-161711400	Enhancers	GM12878-XiMat	blood
26	chr1:161710400-161711600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:161710800-161711400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:161710800-161711600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:161711000-161711400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:161711000-161711400	Enhancers	Dnd41	blood
31	chr1:161711200-161711400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:161711200-161711400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:161711200-161711400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr1:161711200-161711400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:161711200-161711400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:161711200-161711400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:161711200-161711400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:161711200-161711400	Enhancers	A549	lung
39	chr1:161711200-161714200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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