Variant report

Variant	rs11629945
Chromosome Location	chr15:78259248-78259249
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	CEBPD	chr15:78259066-78259585	K562	blood:	n/a	n/a
2	CTCF	chr15:78259165-78259403	A549	lung:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
3	SMC3	chr15:78259095-78259945	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr15:78259165-78259442	MCF-7	breast:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
5	CTCF	chr15:78259153-78259443	GM13977	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
6	CTCF	chr15:78259190-78259435	HepG2	liver:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
7	CTCF	chr15:78259220-78259370	WI-38	lung:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
8	CTCF	chr15:78259150-78259472	Spleen_OC	spleen:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
9	GATA2	chr15:78259146-78259510	K562	blood:	n/a	n/a
10	CTCF	chr15:78259220-78259370	GM12872	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
11	CTCF	chr15:78259200-78259350	HCT-116	colon:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
12	CTCF	chr15:78259178-78259466	HUVEC	blood vessel:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
13	GATA3	chr15:78259210-78259545	MCF-7	breast:	n/a	n/a
14	CTCF	chr15:78259220-78259370	GM12874	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
15	RAD21	chr15:78258940-78259696	HCT-116	colon:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
16	CTCF	chr15:78259240-78259390	HCPEpiC	choroid plexus:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
17	RAD21	chr15:78259069-78259534	SK-N-SH_RA	brain:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
18	CTCF	chr15:78259220-78259370	BE2_C	brain:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
19	GATA3	chr15:78258999-78259743	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr15:78259240-78259390	HAc	cerebellar:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
21	CTCF	chr15:78259064-78259510	HepG2	liver:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
22	CTCF	chr15:78259240-78259390	HCFaa	heart:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
23	CTCF	chr15:78259240-78259390	GM12873	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
24	CTCF	chr15:78259199-78259392	H1-hESC	embryonic stem cell:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
25	CTCF	chr15:78259200-78259350	RPTEC	kidney:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
26	CTCF	chr15:78259087-78259411	H1-hESC	embryonic stem cell:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
27	CTCF	chr15:78259097-78259528	GM12878	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
28	RAD21	chr15:78259159-78259414	K562	blood:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
29	RAD21	chr15:78259131-78259492	A549	lung:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
30	CTCF	chr15:78259220-78259370	AG04449	skin:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
31	RAD21	chr15:78259026-78259537	H1-hESC	embryonic stem cell:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
32	CTCF	chr15:78259240-78259390	MCF-7	breast:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
33	CTCF	chr15:78259180-78259330	GM12869	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
34	CTCF	chr15:78259220-78259370	HRE	kidney:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
35	CTCF	chr15:78259240-78259390	HVMF	connective:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
36	CTCF	chr15:78259200-78259350	K562	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
37	POLR2A	chr15:78259227-78259285	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr15:78259200-78259350	GM12867	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
39	ARID3A	chr15:78259164-78259527	HepG2	liver:	n/a	n/a
40	CTCF	chr15:78259173-78259471	ECC-1	luminal epithelium:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
41	CTCF	chr15:78259179-78259421	GM10266	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
42	CTCF	chr15:78259240-78259390	A549	lung:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
43	CTCF	chr15:78259164-78259422	Fibrobl	skin:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
44	RAD21	chr15:78259178-78259515	H1-hESC	embryonic stem cell:	n/a	chr15:78259308-78259322 chr15:78259307-78259326
45	CTCF	chr15:78259200-78259350	GM12868	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
46	CTCF	chr15:78259160-78259310	A549	lung:	n/a	n/a
47	CTCF	chr15:78259240-78259390	AG09319	gingival:	n/a	chr15:78259306-78259324 chr15:78259308-78259329
48	SMC3	chr15:78259095-78259763	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr15:78259083-78259466	GM12878	blood:	n/a	chr15:78259439-78259448
50	CTCF	chr15:78259188-78259406	GM12891	blood:	n/a	chr15:78259306-78259324 chr15:78259308-78259329

No.	Distal block	Cell Line	Cell type
1	chr15:78258415..78260755-chr15:78280770..78282867,2	MCF-7	breast:
2	chr15:78258734..78259532-chr15:78279301..78280081,2	MCF-7	breast:
3	chr15:78258912..78259522-chr15:78292151..78292959,2	MCF-7	breast:
4	chr15:78258802..78259810-chr15:78400203..78401702,8	MCF-7	breast:
5	chr15:78259091..78259732-chr15:78286600..78287504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261403	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11634206	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634395	0.88[ASN][1000 genomes]
rs11635760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592202	0.84[ASN][1000 genomes]
rs12592545	0.87[ASN][1000 genomes]
rs12595255	0.87[ASN][1000 genomes]
rs12899446	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12907842	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34032999	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35455294	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36046658	0.82[ASN][1000 genomes]
rs4528536	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164210	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175950	0.89[CEU][hapmap]

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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11629945	RP11-114H24.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78258800-78275200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:78259000-78259600	Enhancers	Colon Smooth Muscle	Colon
3	chr15:78259200-78259600	Enhancers	Hela-S3	cervix
4	chr15:78259200-78261600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links