Variant report

Variant	rs2999547
Chromosome Location	chr1:152002663-152002664
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152001004..152003518-chr1:152088501..152090154,2	MCF-7	breast:
2	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
3	chr1:151906991..151909574-chr1:152001582..152003967,2	K562	blood:
4	chr1:151896761..151899276-chr1:152001474..152003211,2	MCF-7	breast:
5	chr1:151798310..151800622-chr1:152001051..152003232,2	K562	blood:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000143365	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11578030	1.00[CHB][hapmap]
rs12123975	0.91[TSI][hapmap]
rs12134184	0.91[TSI][hapmap]
rs1496037	0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs2999536	1.00[CHB][hapmap]
rs2999550	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2999551	0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2999552	1.00[JPT][hapmap]
rs2999553	0.87[ASN][1000 genomes]
rs2999554	0.87[ASN][1000 genomes]
rs2999555	1.00[JPT][hapmap]
rs2999559	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2999562	0.87[ASN][1000 genomes]
rs3007671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3007672	0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3007673	0.87[ASN][1000 genomes]
rs3007674	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007676	1.00[JPT][hapmap]
rs3007678	0.87[ASN][1000 genomes]
rs3007679	1.00[JPT][hapmap]
rs3007704	1.00[CHB][hapmap]
rs3122300	1.00[JPT][hapmap]
rs3122301	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3122303	0.87[ASN][1000 genomes]
rs3122304	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2999547	SELENBP1	cis	cerebellum	SCAN
rs2999547	S100A8	cis	parietal	SCAN
rs2999547	S100A10	cis	cerebellum	SCAN
rs2999547	LASS2	cis	parietal	SCAN
rs2999547	LCE2C	cis	cerebellum	SCAN
rs2999547	PSMB4	cis	cerebellum	SCAN
rs2999547	KCNK5	trans	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151988600-152004000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:151993400-152003000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:151994400-152003200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:151996600-152004400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:151996800-152004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:151997000-152003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:151997000-152004200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:151997000-152004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:151997000-152004800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:151997800-152003200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:151997800-152003400	Weak transcription	Lung	lung
15	chr1:151998600-152003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:151998800-152002800	Enhancers	HMEC	breast
17	chr1:151999000-152004200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:151999400-152004000	Weak transcription	Aorta	Aorta
19	chr1:151999600-152003400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:151999600-152003400	Weak transcription	NH-A	brain
21	chr1:152000000-152004000	Weak transcription	NHLF	lung
22	chr1:152000200-152005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:152000400-152004200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:152000400-152004600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:152000600-152003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:152000600-152003200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:152000600-152003400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:152000800-152003400	Weak transcription	Fetal Intestine Large	intestine
29	chr1:152000800-152003600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:152000800-152004000	Weak transcription	Fetal Kidney	kidney
31	chr1:152001000-152002800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:152001000-152003200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:152001000-152003200	Enhancers	Dnd41	blood
34	chr1:152001000-152003200	Weak transcription	HUVEC	blood vessel
35	chr1:152001200-152002800	Enhancers	Adipose Nuclei	Adipose
36	chr1:152001200-152003000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:152001200-152004000	Weak transcription	Fetal Lung	lung
38	chr1:152001200-152004600	Weak transcription	Spleen	Spleen
39	chr1:152001400-152002800	Enhancers	NHDF-Ad	bronchial
40	chr1:152001400-152003000	Enhancers	Hela-S3	cervix
41	chr1:152001400-152003200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:152001400-152003200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:152001400-152003200	Weak transcription	Left Ventricle	heart
44	chr1:152001400-152003200	Weak transcription	Thymus	Thymus
45	chr1:152001400-152003200	Enhancers	NHEK	skin
46	chr1:152001400-152003400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:152001600-152002800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:152001600-152003400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:152001600-152003600	Weak transcription	Fetal Stomach	stomach
50	chr1:152001600-152005000	Strong transcription	Primary T cells from cord blood	blood

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