Variant report

Variant	rs5753410
Chromosome Location	chr22:31376009-31376010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr22:31375967-31376260	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr22:31375771-31376187	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr22:31375794-31376023	Hela-S3	cervix:	n/a	n/a
4	MTA3	chr22:31375855-31376606	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:31375989-31376339	HL-60	blood:	n/a	n/a
6	CTCF	chr22:31376000-31376150	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:31375919-31376711	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr22:31375871-31376132	ProgFib	skin:	n/a	n/a
9	RUNX3	chr22:31375904-31376383	GM12878	blood:	n/a	n/a
10	POLR2A	chr22:31375817-31377149	MCF-7	breast:	n/a	n/a
11	RUNX3	chr22:31375930-31376329	GM12878	blood:	n/a	n/a
12	POLR2A	chr22:31376007-31376213	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr22:31375863-31376610	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr22:31375918-31376833	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr22:31375927-31376965	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr22:31375798-31376560	U87	brain:	n/a	n/a
17	SETDB1	chr22:31375502-31376713	U2OS	brain:	n/a	n/a
18	FOSL2	chr22:31375981-31376326	HepG2	liver:	n/a	chr22:31376183-31376191 chr22:31376184-31376191
19	POLR2A	chr22:31375959-31376534	HCT-116	colon:	n/a	n/a
20	POLR2A	chr22:31375861-31376811	PBDE	blood:	n/a	n/a
21	POLR2A	chr22:31373217-31377074	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr22:31375990-31376611	U87	brain:	n/a	n/a
23	POLR2A	chr22:31375792-31376636	U87	brain:	n/a	n/a
24	POLR2A	chr22:31375791-31376800	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr22:31376000-31376150	HBMEC	blood vessel:	n/a	n/a
26	POLR2A	chr22:31375722-31376743	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr22:31375881-31376138	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr22:31375657-31376635	GM12878	blood:	n/a	n/a
29	POLR2A	chr22:31375931-31376160	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr22:31375971-31376641	U87	brain:	n/a	n/a
31	POLR2A	chr22:31375888-31376647	HepG2	liver:	n/a	n/a
32	POLR2A	chr22:31375924-31376391	HepG2	liver:	n/a	n/a
33	BATF	chr22:31375983-31376253	GM12878	blood:	n/a	n/a
34	CTCF	chr22:31375960-31376110	HCPEpiC	choroid plexus:	n/a	n/a
35	POLR2A	chr22:31375699-31376246	K562	blood:	n/a	n/a
36	POLR2A	chr22:31368958-31378923	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr22:31375979-31377161	HepG2	liver:	n/a	n/a
38	POLR2A	chr22:31369206-31376719	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31375047..31376571-chr22:31391886..31394125,2	MCF-7	breast:
2	chr22:31375006..31378537-chr22:31476924..31478681,3	MCF-7	breast:
3	chr22:31371236..31374508-chr22:31375496..31377845,5	K562	blood:
4	chr22:31371775..31374026-chr22:31375760..31377892,3	K562	blood:
5	chr22:31375745..31378647-chr22:31380130..31383422,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269972	TF binding region
ENSG00000269987	TF binding region
ENSG00000183963	Chromatin interaction
ENSG00000269972	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1003480	0.86[YRI][hapmap]
rs1005252	0.97[YRI][hapmap]
rs10854601	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11089484	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12167144	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12168307	0.82[AMR][1000 genomes]
rs1807686	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2016654	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2019171	0.82[AFR][1000 genomes]
rs2019182	0.83[EUR][1000 genomes]
rs2072132	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2074578	0.93[YRI][hapmap]
rs2079221	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2240175	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240177	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240179	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240180	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240182	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2240183	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285918	0.97[YRI][hapmap];0.80[AFR][1000 genomes]
rs3747151	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788426	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804084	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804085	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3827330	0.81[EUR][1000 genomes]
rs3948685	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820916	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820921	0.81[EUR][1000 genomes]
rs4820923	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820925	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4820926	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5749185	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5749186	0.93[YRI][hapmap]
rs5749189	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749192	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749199	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5749201	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753369	0.93[YRI][hapmap]
rs5753383	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753386	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753389	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753394	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753396	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753398	0.97[YRI][hapmap]
rs5753407	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753408	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997807	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5997830	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997838	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5997846	0.96[YRI][hapmap]
rs6518726	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6518729	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs722683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722684	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7284767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7289831	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7290078	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7291077	0.80[AFR][1000 genomes]
rs7291199	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7291361	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7291471	0.81[EUR][1000 genomes]
rs737924	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737926	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs737927	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs739896	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8004	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8135974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609183	0.95[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9609185	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9609188	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9609193	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5753410	MORC2-AS1	cis	Thyroid	GTEx
rs5753410	MORC2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs5753410	TUG1	Cis_1M	lymphoblastoid	RTeQTL
rs5753410	MORC2-AS1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31366400-31376800	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr22:31366600-31376400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr22:31366800-31380800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:31371800-31376200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr22:31372000-31376200	Weak transcription	NH-A	brain
6	chr22:31373000-31381800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:31374200-31376800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr22:31374400-31384000	Weak transcription	HSMMtube	muscle
9	chr22:31374600-31376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:31374600-31379200	Weak transcription	HSMM	muscle
11	chr22:31374800-31378000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:31375000-31377200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:31375800-31376200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr22:31375800-31376600	Enhancers	HepG2	liver
15	chr22:31376000-31376200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:31376000-31376200	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links