Variant report

Variant	rs41307646
Chromosome Location	chr1:213025689-213025690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr1:213025497-213025766	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr1:213025459-213025706	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr1:213025393-213025755	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr1:213025437-213025748	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:213025515-213025741	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr1:213025457-213025806	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr1:213025373-213025890	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF2	chr1:213025410-213025857	H1-hESC	embryonic stem cell:	n/a	n/a
9	NANOG	chr1:213025443-213025779	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:213025453-213025817	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr1:213025544-213025890	H1-hESC	embryonic stem cell:	n/a	n/a
12	HDAC2	chr1:213025425-213025830	H1-hESC	embryonic stem cell:	n/a	chr1:213025429-213025443 chr1:213025427-213025441 chr1:213025426-213025440 chr1:213025431-213025445 chr1:213025425-213025439
13	TCF12	chr1:213025421-213025789	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr1:213025420-213025772	H1-hESC	embryonic stem cell:	n/a	chr1:213025426-213025440
15	SP1	chr1:213025415-213025842	H1-hESC	embryonic stem cell:	n/a	n/a
16	GTF2F1	chr1:213025473-213025798	H1-hESC	embryonic stem cell:	n/a	n/a
17	SP4	chr1:213025463-213025823	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUND	chr1:213025473-213025760	H1-hESC	embryonic stem cell:	n/a	n/a
19	POU5F1	chr1:213025418-213025885	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf227-1	chr1:213025450-213027653	ENSG00000198468
2	lnc-C1orf227-1	chr1:213025450-213027651	ENSG00000198468.3
3	lnc-FLVCR1-1	chr1:213025477-213026496	NONHSAT009406

No data

Variant related genes	Relation type
C1orf227	TF binding region
ENSG00000235182	TF binding region
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2047288	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047291	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2088256	1.00[AFR][1000 genomes]
rs3768549	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41258005	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296678	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296680	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41297452	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300027	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300033	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300035	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300043	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300979	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41301029	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41307644	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41314542	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58746017	0.92[EUR][1000 genomes];1.00[ASN][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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv3413107	chr1:213021779-213025977	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers 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	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213020400-213028600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:213021600-213026800	Weak transcription	HepG2	liver
3	chr1:213022600-213030000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:213024200-213030000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:213024200-213030200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:213024600-213026800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:213025200-213030200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:213025400-213029600	Weak transcription	Dnd41	blood
9	chr1:213025600-213026600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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