Variant report

Variant	rs1530484
Chromosome Location	chr8:8907294-8907295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8907031..8909289-chr8:9008104..9009866,2	K562	blood:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction
ENSG00000253426	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10087416	1.00[CHB][hapmap]
rs10091588	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036082	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774244	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775788	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779660	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779804	1.00[ASN][1000 genomes]
rs11780338	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780774	1.00[ASN][1000 genomes]
rs11781203	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782835	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11784750	1.00[ASN][1000 genomes]
rs13250781	1.00[ASN][1000 genomes]
rs13263364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13277114	1.00[ASN][1000 genomes]
rs17155334	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17155367	1.00[ASN][1000 genomes]
rs17646197	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17700611	1.00[ASN][1000 genomes]
rs17701980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510464	0.82[EUR][1000 genomes]
rs28520356	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572014	1.00[ASN][1000 genomes]
rs34293316	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840376	1.00[ASN][1000 genomes]
rs4840391	1.00[ASN][1000 genomes]
rs55824072	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109025	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349323	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400435	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57280925	1.00[ASN][1000 genomes]
rs59041878	1.00[ASN][1000 genomes]
rs59257214	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60551984	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61397430	1.00[ASN][1000 genomes]
rs61730232	1.00[ASN][1000 genomes]
rs62492947	1.00[ASN][1000 genomes]
rs62493173	0.81[EUR][1000 genomes]
rs62493174	1.00[ASN][1000 genomes]
rs62495491	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62495539	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601282	1.00[CHB][hapmap]
rs6601292	1.00[ASN][1000 genomes]
rs6981610	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6981745	1.00[ASN][1000 genomes]
rs6982619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6987569	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996374	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001187	1.00[ASN][1000 genomes]
rs73518330	1.00[ASN][1000 genomes]
rs73518392	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357482	1.00[ASN][1000 genomes]
rs73662247	1.00[ASN][1000 genomes]
rs7822129	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826478	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828944	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830266	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7843024	1.00[ASN][1000 genomes]
rs7843154	1.00[ASN][1000 genomes]
rs7843369	1.00[ASN][1000 genomes]
rs7843789	1.00[ASN][1000 genomes]
rs7846007	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895253	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9329176	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987276	0.92[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1530484	SGK223	cis	cerebellum	SCAN
rs1530484	DEFB136	cis	parietal	SCAN
rs1530484	CLDN23	cis	multi-tissue	Pritchard
rs1530484	MFHAS1	cis	cerebellum	SCAN
rs1530484	CTSB	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
2	chr8:8888400-8910800	Weak transcription	Hela-S3	cervix
3	chr8:8891000-8914800	Weak transcription	Fetal Stomach	stomach
4	chr8:8891400-8915200	Weak transcription	K562	blood
5	chr8:8893800-8913800	Weak transcription	Primary T cells from cord blood	blood
6	chr8:8898600-8908800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr8:8899000-8919200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:8903200-8910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:8905600-8910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:8905800-8911000	Weak transcription	Fetal Lung	lung
11	chr8:8906200-8913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:8906200-8914600	Weak transcription	Fetal Muscle Leg	muscle
13	chr8:8907000-8907400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr8:8907000-8907400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr8:8907000-8907400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr8:8907000-8907600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr8:8907000-8907600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr8:8907200-8907600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr8:8907200-8907600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr8:8907200-8907600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr8:8907200-8907600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:8907200-8907600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:8907200-8907800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr8:8907200-8909400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links