Variant report

Variant	rs17522524
Chromosome Location	chr1:226829990-226829991
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	chr1:226828494..226832604-chr1:226851440..226853779,3	K562	blood:
2	chr1:226829138..226831171-chr1:226838507..226841235,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1144838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1144839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1144840	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1288936	0.85[JPT][hapmap]
rs17588687	0.89[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768376	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820635	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820637	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs697843	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533764	0.81[EUR][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	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak 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	3 gene(s)	inside rSNPs	diseases
5	nsv516277	chr1:226825341-226833304	Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17522524	HIST3H2BB	cis	cerebellum	SCAN
rs17522524	CABC1	cis	cerebellum	SCAN
rs17522524	PARP1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
2	chr1:226814800-226830400	Strong transcription	Thymus	Thymus
3	chr1:226814800-226834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
5	chr1:226816800-226837000	Weak transcription	Fetal Brain Male	brain
6	chr1:226817000-226837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:226817200-226830600	Strong transcription	Fetal Intestine Small	intestine
8	chr1:226819200-226830200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:226820400-226840800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr1:226820800-226831000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:226822000-226833400	Weak transcription	Fetal Heart	heart
12	chr1:226823200-226830000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:226823200-226834800	Weak transcription	Fetal Kidney	kidney
14	chr1:226823200-226841400	Weak transcription	NHDF-Ad	bronchial
15	chr1:226823400-226834400	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr1:226823600-226830000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:226823600-226830600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:226823600-226831000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:226823800-226830400	Weak transcription	HMEC	breast
20	chr1:226823800-226830600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:226823800-226830600	Strong transcription	Esophagus	oesophagus
22	chr1:226823800-226830600	Weak transcription	Stomach Mucosa	stomach
23	chr1:226823800-226830600	Weak transcription	NHEK	skin
24	chr1:226823800-226837400	Strong transcription	Dnd41	blood
25	chr1:226824000-226834800	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:226824200-226830000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:226824200-226830800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:226824200-226830800	Strong transcription	Gastric	stomach
29	chr1:226824400-226830400	Strong transcription	Fetal Thymus	thymus
30	chr1:226824800-226830400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:226824800-226836800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:226825000-226830000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:226825000-226834200	Weak transcription	Liver	Liver
34	chr1:226825200-226830400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:226825200-226830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:226825200-226830800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:226825400-226830400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:226825400-226830600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:226825400-226830600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:226825400-226830800	Weak transcription	NHLF	lung
41	chr1:226825600-226830000	Genic enhancers	Brain Substantia Nigra	brain
42	chr1:226825800-226834000	Genic enhancers	Brain Anterior Caudate	brain
43	chr1:226826000-226830200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:226826400-226830000	Strong transcription	Pancreas	Pancrea
45	chr1:226826400-226830600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:226826600-226830600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:226826600-226830600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:226826600-226830800	Weak transcription	HSMM	muscle
49	chr1:226826600-226833000	Weak transcription	Psoas Muscle	Psoas
50	chr1:226826600-226833600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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