Variant report

Variant	rs636291
Chromosome Location	chr1:10556097-10556098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10488833..10492668-chr1:10552829..10556296,4	MCF-7	breast:
2	chr1:10437389..10440210-chr1:10554525..10556492,2	K562	blood:
3	chr1:10555587..10558317-chr1:10561654..10564400,3	K562	blood:
4	chr1:10536268..10539627-chr1:10553457..10556201,3	K562	blood:
5	chr1:10488234..10492176-chr1:10552870..10556900,4	K562	blood:
6	chr1:10488879..10492501-chr1:10553959..10556720,6	MCF-7	breast:
7	chr1:10533760..10535685-chr1:10553523..10556156,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251503	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000271989	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10864458	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864459	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10864460	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs1152739	0.84[EUR][1000 genomes]
rs1188525	0.87[EUR][1000 genomes]
rs1188526	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1188529	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12375	0.80[GIH][hapmap]
rs1411402	0.86[CEU][hapmap]
rs1632108	0.86[EUR][1000 genomes]
rs2056417	0.86[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs2480777	0.80[GIH][hapmap]
rs2483677	0.86[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2506901	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2506902	0.95[CEU][hapmap]
rs2781230	0.95[CEU][hapmap]
rs2781232	0.87[EUR][1000 genomes]
rs2847344	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs585870	0.95[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs587916	0.87[EUR][1000 genomes]
rs589400	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs596537	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs597438	0.87[EUR][1000 genomes]
rs607941	0.95[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs616402	0.86[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs620405	0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs622623	0.95[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs648324	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs648399	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs652771	0.87[EUR][1000 genomes]
rs6540933	0.87[EUR][1000 genomes]
rs660725	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs662064	0.95[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6658216	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs668805	0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs669701	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs683864	0.86[EUR][1000 genomes]
rs685746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	25217961	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs636291	PLEKHG5	cis	parietal	SCAN
rs636291	AADACL3	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10553000-10567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:10554000-10557000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:10554600-10556400	Genic enhancers	Fetal Intestine Small	intestine
4	chr1:10554600-10556600	Enhancers	Fetal Heart	heart
5	chr1:10554600-10556800	Enhancers	Left Ventricle	heart
6	chr1:10554800-10556200	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:10554800-10556400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr1:10554800-10556400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:10554800-10556600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr1:10554800-10556800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:10554800-10568600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:10555000-10556400	Enhancers	Gastric	stomach
13	chr1:10555000-10556600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:10555000-10556600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:10555000-10556600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:10555000-10556800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr1:10555000-10556800	Flanking Active TSS	NHEK	skin
18	chr1:10555200-10556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:10555200-10556600	Flanking Active TSS	HMEC	breast
20	chr1:10555200-10567400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:10555200-10567400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:10555200-10567400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:10555200-10568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:10555200-10568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:10555200-10570000	Weak transcription	Aorta	Aorta
26	chr1:10555400-10556400	Strong transcription	Hela-S3	cervix
27	chr1:10555400-10557600	Strong transcription	HepG2	liver
28	chr1:10555400-10567200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:10555400-10567400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:10555600-10556200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:10555600-10556200	Enhancers	Primary B cells from cord blood	blood
32	chr1:10555600-10556200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:10555600-10556200	Weak transcription	Adipose Nuclei	Adipose
34	chr1:10555600-10556200	Enhancers	Fetal Thymus	thymus
35	chr1:10555600-10556200	Weak transcription	Right Atrium	heart
36	chr1:10555600-10556200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:10555600-10556200	Enhancers	Small Intestine	intestine
38	chr1:10555600-10556200	Weak transcription	NHLF	lung
39	chr1:10555600-10556400	Enhancers	Fetal Kidney	kidney
40	chr1:10555600-10556600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:10555600-10556600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:10555600-10556600	Enhancers	Stomach Mucosa	stomach
43	chr1:10555600-10556600	Strong transcription	K562	blood
44	chr1:10555600-10557400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:10555600-10557600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:10555600-10557600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:10555600-10557600	Strong transcription	Fetal Stomach	stomach
48	chr1:10555600-10557800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:10555600-10557800	Strong transcription	Brain Germinal Matrix	brain
50	chr1:10555600-10558600	Weak transcription	Primary hematopoietic stem cells	blood

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