Variant report

Variant	rs5994368
Chromosome Location	chr22:31456863-31456864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RPC155	chr22:31456794-31457863	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31363691..31369255-chr22:31456002..31460514,7	MCF-7	breast:
2	chr22:31363469..31366268-chr22:31450278..31456884,6	MCF-7	breast:
3	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
4	chr22:31455775..31461842-chr22:31476267..31480955,13	MCF-7	breast:

Variant related genes	Relation type
SMTN	TF binding region
ENSG00000253352	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000133422	Chromatin interaction
ENSG00000273387	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10427701	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10854603	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11705177	0.97[ASN][1000 genomes]
rs11705250	0.97[ASN][1000 genomes]
rs11705313	0.97[ASN][1000 genomes]
rs11705396	0.86[ASN][1000 genomes]
rs12157450	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12157641	0.81[EUR][1000 genomes]
rs12165471	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170984	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12330058	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053618	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13057068	0.97[ASN][1000 genomes]
rs2006301	1.00[ASN][1000 genomes]
rs35060453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753456	0.81[EUR][1000 genomes]
rs5994365	0.90[ASN][1000 genomes]
rs5994370	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997863	0.97[ASN][1000 genomes]
rs5997864	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5997866	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5997871	0.90[ASN][1000 genomes]
rs5997872	0.85[ASN][1000 genomes]
rs7284593	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7291565	0.95[ASN][1000 genomes]
rs7292038	0.97[ASN][1000 genomes]
rs7292982	0.84[ASN][1000 genomes]
rs9619166	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9619167	0.97[ASN][1000 genomes]
rs9621175	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription 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	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv964620	chr22:31452981-31465140	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv962852	chr22:31455516-31465140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5994368	MORC2-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31452000-31458000	Weak transcription	Adipose Nuclei	Adipose
2	chr22:31452800-31458200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr22:31455400-31458400	Enhancers	K562	blood
4	chr22:31455600-31457000	Enhancers	HepG2	liver
5	chr22:31455600-31457600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr22:31455800-31457400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:31455800-31458400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr22:31456000-31458200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr22:31456000-31458200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr22:31456000-31458200	Weak transcription	HMEC	breast
11	chr22:31456200-31457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:31456200-31460000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:31456200-31460000	Weak transcription	A549	lung
14	chr22:31456400-31458200	Weak transcription	Fetal Intestine Large	intestine
15	chr22:31456400-31458400	Weak transcription	Fetal Intestine Small	intestine
16	chr22:31456600-31457200	Enhancers	NHEK	skin
17	chr22:31456600-31461000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr22:31456800-31457000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:31456800-31457400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:31456800-31457400	Enhancers	Hela-S3	cervix
21	chr22:31456800-31458800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links