Variant report

Variant	rs2530658
Chromosome Location	chr22:29995718-29995719
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	chr22:29993439..29997077-chr22:29997568..30000829,3	MCF-7	breast:
2	chr22:29995484..29998034-chr22:30003298..30004974,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction
ENSG00000233010	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1006396	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10427824	0.80[EUR][1000 genomes]
rs11705569	0.88[ASN][1000 genomes]
rs16987832	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987839	0.87[ASN][1000 genomes]
rs2247753	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2530656	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530664	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2531848	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531849	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425992	0.84[ASN][1000 genomes]
rs433194	0.82[ASN][1000 genomes]
rs456585	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs458196	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459450	0.83[ASN][1000 genomes]
rs460428	0.84[ASN][1000 genomes]
rs460994	0.83[ASN][1000 genomes]
rs462444	0.85[ASN][1000 genomes]
rs463220	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468254	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs468475	0.82[ASN][1000 genomes]
rs468692	0.82[ASN][1000 genomes]
rs468795	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468852	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469230	0.82[ASN][1000 genomes]
rs469253	0.82[ASN][1000 genomes]
rs469295	0.81[ASN][1000 genomes]
rs469363	0.82[ASN][1000 genomes]
rs469565	0.81[ASN][1000 genomes]
rs5763305	0.80[EUR][1000 genomes]
rs5763349	0.83[ASN][1000 genomes]
rs57995869	0.81[EUR][1000 genomes]
rs695525	0.85[ASN][1000 genomes]
rs695780	0.82[ASN][1000 genomes]
rs695816	0.85[ASN][1000 genomes]
rs73159040	0.88[ASN][1000 genomes]
rs7609	0.82[ASN][1000 genomes]
rs8135828	0.82[EUR][1000 genomes]
rs8141518	0.88[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2530658	THOC5	cis	Artery Aorta	GTEx
rs2530658	THOC5	cis	Artery Tibial	GTEx
rs2530658	THOC5	cis	Thyroid	GTEx
rs2530658	THOC5	cis	Nerve Tibial	GTEx
rs2530658	NIPSNAP1	cis	Stomach	GTEx
rs2530658	THOC5	cis	lung	GTEx
rs2530658	THOC5	cis	Adipose Subcutaneous	GTEx
rs2530658	THOC5	cis	Muscle Skeletal	GTEx
rs2530658	THOC5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29977600-29998800	Weak transcription	Right Atrium	heart
2	chr22:29985200-29999000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr22:29985200-29999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:29990200-29999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:29992800-29999000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr22:29993200-29997800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr22:29993400-29999000	Weak transcription	HSMMtube	muscle
8	chr22:29993600-29999000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr22:29994600-29995800	Enhancers	Fetal Intestine Small	intestine
10	chr22:29994800-29997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:29995000-29998600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr22:29995000-29999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:29995000-29999000	Weak transcription	Colon Smooth Muscle	Colon
14	chr22:29995000-29999000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr22:29995000-29999000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr22:29995400-29999000	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links