Variant report

Variant	rs7529904
Chromosome Location	chr1:85490566-85490567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:85490439-85490715	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:85490512-85490716	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:85490536-85490653	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:85490535-85490666	HepG2	liver:	n/a	n/a
5	CTCF	chr1:85490460-85490610	HVMF	connective:	n/a	n/a
6	CTCF	chr1:85490500-85490650	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr1:85490480-85490630	HMEC	breast:	n/a	n/a
8	CTCF	chr1:85490520-85490670	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:85490560-85490710	HCT-116	colon:	n/a	n/a
10	CTCF	chr1:85490475-85490746	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr1:85490480-85490630	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr1:85490460-85490794	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr1:85490474-85490751	MCF-7	breast:	n/a	n/a
14	CTCF	chr1:85490565-85490647	GM19238	blood:	n/a	n/a
15	CTCF	chr1:85490550-85490662	NHEK	skin:	n/a	n/a
16	CTCF	chr1:85490439-85490704	T-47D	breast:	n/a	n/a
17	CTCF	chr1:85490540-85490690	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:85490461-85490708	GM12878	blood:	n/a	n/a
19	CTCF	chr1:85490500-85490650	HPF	lung:	n/a	n/a
20	CTCF	chr1:85490470-85490766	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr1:85490525-85490668	MCF-7	breast:	n/a	n/a
22	CTCF	chr1:85490480-85490630	HEEpiC	esophagus:	n/a	n/a
23	CTCF	chr1:85490563-85490684	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr1:85490520-85490670	HPAF	blood vessel:	n/a	n/a
25	CTCF	chr1:85490480-85490630	HMF	breast:	n/a	n/a
26	CTCF	chr1:85490511-85490656	K562	blood:	n/a	n/a
27	RAD21	chr1:85490429-85490832	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:85490520-85490670	HCT-116	colon:	n/a	n/a
29	CTCF	chr1:85490460-85490610	HMEC	breast:	n/a	n/a
30	CTCF	chr1:85490460-85490610	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr1:85490556-85490627	MCF-7	breast:	n/a	n/a
32	MAX	chr1:85490513-85490753	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr1:85490458-85490745	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	chr1:85410128..85411315-chr1:85490122..85491874,8	MCF-7	breast:

No data

Variant related genes	Relation type
MCOLN3	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10782538	1.00[CHB][hapmap]
rs11161512	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs11161516	1.00[CHB][hapmap]
rs17099213	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap]
rs17119333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120570	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap]
rs1962897	0.85[EUR][1000 genomes]
rs41383647	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41461649	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4907127	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs55640042	0.80[ASN][1000 genomes]
rs55663547	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55814348	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101051	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314577	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576745	1.00[CHB][hapmap]
rs6576747	1.00[CHB][hapmap]
rs6681402	1.00[CHB][hapmap]
rs6681619	1.00[CHB][hapmap]
rs6684766	1.00[CHB][hapmap]
rs6695223	1.00[CHB][hapmap]
rs6697585	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs898035	1.00[CHB][hapmap]

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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7529904	MCOLN2	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85483600-85494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:85485400-85491400	Strong transcription	Fetal Intestine Large	intestine
3	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
4	chr1:85485800-85505200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:85486000-85513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:85486400-85499200	Weak transcription	NHDF-Ad	bronchial
7	chr1:85486400-85500400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:85487800-85490800	Strong transcription	Fetal Intestine Small	intestine
9	chr1:85488000-85493000	Weak transcription	HMEC	breast
10	chr1:85488800-85493000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:85489000-85492600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:85489000-85492600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:85489000-85500000	Weak transcription	Adipose Nuclei	Adipose
14	chr1:85490400-85490800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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