Variant report

Variant	rs73546883
Chromosome Location	chr6:133858259-133858260
allele	C/T
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	SMC3	chr6:133858048-133858353	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:133857936-133859040	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr6:133858247-133858647	A549	lung:	n/a	n/a
4	CTCF	chr6:133858173-133858282	GM12878	blood:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
5	CTCF	chr6:133858160-133858310	HPAF	blood vessel:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
6	CTCF	chr6:133858153-133858285	Gliobla	brain:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
7	CTCF	chr6:133858167-133858279	A549	lung:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
8	RAD21	chr6:133858041-133858373	H1-hESC	embryonic stem cell:	n/a	chr6:133858185-133858204 chr6:133858189-133858203
9	RAD21	chr6:133858219-133858268	A549	lung:	n/a	n/a
10	CTCF	chr6:133858180-133858330	BE2_C	brain:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
11	CTCF	chr6:133858180-133858330	HCPEpiC	choroid plexus:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
12	CTCF	chr6:133858220-133858370	MCF-7	breast:	n/a	n/a
13	CTCF	chr6:133858018-133858367	HCT-116	colon:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
14	CTCF	chr6:133858160-133858310	NB4	blood:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
15	CTCF	chr6:133858140-133858290	NHLF	lung:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
16	CTCF	chr6:133858135-133858296	MCF-7	breast:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
17	CTCF	chr6:133858108-133858306	A549	lung:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
18	RAD21	chr6:133858046-133858373	Hela-S3	cervix:	n/a	chr6:133858185-133858204 chr6:133858189-133858203
19	CTCF	chr6:133858178-133858280	MCF-7	breast:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
20	CTCF	chr6:133858132-133858272	Hela-S3	cervix:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
21	CTCF	chr6:133858120-133858270	HBMEC	blood vessel:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
22	CTCF	chr6:133858125-133858300	MCF-7	breast:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
23	CTCF	chr6:133858200-133858350	HPF	lung:	n/a	n/a
24	CTCF	chr6:133858220-133858370	RPTEC	kidney:	n/a	n/a
25	RAD21	chr6:133858027-133858302	H1-hESC	embryonic stem cell:	n/a	chr6:133858185-133858204 chr6:133858189-133858203
26	RAD21	chr6:133857970-133858372	H1-hESC	embryonic stem cell:	n/a	chr6:133858185-133858204 chr6:133858189-133858203
27	CTCF	chr6:133858140-133858290	BE2_C	brain:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
28	CTCF	chr6:133858182-133858282	NHEK	skin:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
29	POLR2A	chr6:133854009-133859211	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr6:133858140-133858290	AG04449	skin:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205
31	CTCF	chr6:133858231-133858262	Fibrobl	skin:	n/a	n/a
32	CTCF	chr6:133858200-133858350	HEK293	kidney:	n/a	n/a
33	CTCF	chr6:133858163-133858300	ProgFib	skin:	n/a	chr6:133858189-133858202 chr6:133858182-133858203 chr6:133858187-133858205

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A12-2	chr6:133856918-133858496	ENSG00000227954.2
2	lnc-SLC2A12-2	chr6:133856918-133858496	NR_109982

Variant related genes	Relation type
ENSG00000272428	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs35516420	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3777867	1.00[AMR][1000 genomes]
rs58305346	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59368621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73544958	0.85[AMR][1000 genomes]
rs73544961	1.00[AMR][1000 genomes]
rs73544963	1.00[AMR][1000 genomes]
rs73544978	1.00[AMR][1000 genomes]
rs73544982	1.00[AMR][1000 genomes]
rs73544985	1.00[AMR][1000 genomes]
rs73546816	1.00[AMR][1000 genomes]
rs73546828	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546848	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7748259	0.88[AFR][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	nsv886681	chr6:133833284-133869617	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133823200-133869600	Weak transcription	Psoas Muscle	Psoas
2	chr6:133824400-133861600	Weak transcription	Ovary	ovary
3	chr6:133826600-133862400	Weak transcription	Fetal Lung	lung
4	chr6:133837400-133863600	Weak transcription	A549	lung
5	chr6:133845400-133860400	Weak transcription	HSMMtube	muscle
6	chr6:133854800-133866200	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:133855000-133862800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:133855000-133863200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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