Variant report

Variant	rs1944037
Chromosome Location	chr11:62803525-62803526
allele	C/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	CTCF	chr11:62803111-62803626	HCT-116	colon:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
2	RAD21	chr11:62803065-62803577	SK-N-SH_RA	brain:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
3	CTCF	chr11:62803513-62803660	GM19238	blood:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
4	RAD21	chr11:62803103-62803647	A549	lung:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
5	CTCF	chr11:62803083-62803727	MCF-7	breast:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
6	SMC3	chr11:62803088-62803541	GM12878	blood:	n/a	chr11:62803320-62803334
7	CTCF	chr11:62803129-62803693	MCF-7	breast:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
8	CTCF	chr11:62803400-62803550	HEK293	kidney:	n/a	n/a
9	STAT3	chr11:62803256-62803526	MCF10A-Er-Src	breast:	n/a	chr11:62803393-62803404 chr11:62803395-62803404 chr11:62803394-62803403
10	CTCF	chr11:62803505-62803648	A549	lung:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
11	CTCF	chr11:62803473-62803661	ProgFib	skin:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
12	CTCF	chr11:62803520-62803670	GM12864	blood:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
13	RAD21	chr11:62803025-62803743	MCF-7	breast:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
14	CTCF	chr11:62803101-62803771	HepG2	liver:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
15	CTCF	chr11:62803182-62803669	MCF-7	breast:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
16	CTCF	chr11:62802964-62803777	HCT-116	colon:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
17	CTCF	chr11:62803194-62803677	Fibrobl	skin:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
18	RAD21	chr11:62803131-62803730	HepG2	liver:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
19	RAD21	chr11:62803101-62803554	ECC-1	luminal epithelium:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
20	CTCF	chr11:62803504-62803633	MCF-7	breast:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
21	POLR2A	chr11:62803401-62803541	MCF-7	breast:	n/a	n/a
22	RAD21	chr11:62803152-62803590	K562	blood:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338
23	CTCF	chr11:62803132-62803666	IMR90	lung:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
24	RAD21	chr11:62803100-62803532	GM12878	blood:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
25	ZNF143	chr11:62803158-62803551	GM12878	blood:	n/a	n/a
26	RAD21	chr11:62803124-62803625	H1-hESC	embryonic stem cell:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
27	CTCF	chr11:62803095-62803693	K562	blood:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
28	CTCF	chr11:62803177-62803659	Gliobla	brain:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
29	CEBPB	chr11:62803092-62803562	A549	lung:	n/a	chr11:62803286-62803297
30	CTCF	chr11:62803116-62803661	A549	lung:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
31	CTCF	chr11:62803175-62803666	MCF-7	breast:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
32	CTCF	chr11:62803216-62803657	NHEK	skin:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
33	CTCF	chr11:62803497-62803619	GM10248	blood:	n/a	chr11:62803552-62803565 chr11:62803550-62803568
34	RAD21	chr11:62802914-62803767	HCT-116	colon:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
35	RAD21	chr11:62803021-62803649	H1-hESC	embryonic stem cell:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
36	CTCF	chr11:62803131-62803542	ECC-1	luminal epithelium:	n/a	chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803321-62803334
37	CEBPB	chr11:62803074-62803527	ECC-1	luminal epithelium:	n/a	chr11:62803286-62803297
38	CTCF	chr11:62803191-62803638	T-47D	breast:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
39	CTCF	chr11:62803121-62803669	GM12878	blood:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
40	RAD21	chr11:62803145-62803534	IMR90	lung:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
41	CTCF	chr11:62803110-62803700	K562	blood:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
42	RAD21	chr11:62803080-62803732	A549	lung:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
43	TEAD4	chr11:62803121-62803627	K562	blood:	n/a	chr11:62803315-62803324
44	CTCF	chr11:62803129-62803696	K562	blood:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
45	CEBPB	chr11:62803052-62803598	MCF-7	breast:	n/a	chr11:62803286-62803297
46	RAD21	chr11:62803043-62803692	ECC-1	luminal epithelium:	n/a	chr11:62803321-62803328 chr11:62803323-62803332 chr11:62803319-62803338 chr11:62803145-62803159
47	CTCF	chr11:62803183-62803676	Hela-S3	cervix:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
48	CTCF	chr11:62803104-62803571	H1-hESC	embryonic stem cell:	n/a	chr11:62803552-62803565 chr11:62803318-62803336 chr11:62803320-62803341 chr11:62803319-62803335 chr11:62803323-62803331 chr11:62803550-62803568 chr11:62803321-62803334
49	CEBPB	chr11:62802958-62803702	HCT-116	colon:	n/a	chr11:62803286-62803297
50	CTCF	chr11:62803520-62803641	GM12892	blood:	n/a	chr11:62803552-62803565 chr11:62803550-62803568

No.	Distal block	Cell Line	Cell type
1	chr11:62802846..62803791-chr11:62980023..62980911,6	MCF-7	breast:
2	chr11:62803292..62803814-chr13:91253834..91254354,2	MCF-7	breast:
3	chr11:62802803..62803858-chr11:63041979..63043067,8	MCF-7	breast:
4	chr11:62607769..62610618-chr11:62800892..62803706,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256041	TF binding region
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11231340	0.83[ASN][1000 genomes]
rs11231342	0.83[ASN][1000 genomes]
rs3935736	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124143	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs7130180	0.94[ASN][1000 genomes]
rs7948606	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9971529	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
2	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases
3	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv523357	chr11:62801148-62838511	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1944037	LTBP3	cis	parietal	SCAN
rs1944037	SART1	cis	parietal	SCAN
rs1944037	CDC42BPG	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62803000-62803600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr11:62803000-62803600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:62803000-62803600	Enhancers	Brain Germinal Matrix	brain
4	chr11:62803000-62803600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:62803200-62803600	Active TSS	Stomach Mucosa	stomach
6	chr11:62803400-62803600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr11:62803400-62803600	Enhancers	Liver	Liver
8	chr11:62803400-62803600	Enhancers	Brain Angular Gyrus	brain
9	chr11:62803400-62803600	Enhancers	Brain Anterior Caudate	brain
10	chr11:62803400-62803600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr11:62803400-62803600	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links