Variant report

Variant	rs12041012
Chromosome Location	chr1:85515644-85515645
allele	A/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	chr1:85515540-85515690	GM12873	blood:	n/a	n/a
2	JUND	chr1:85515439-85515762	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr1:85515382-85515773	H1-hESC	embryonic stem cell:	n/a	n/a
4	YY1	chr1:85515435-85515772	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr1:85515386-85515802	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:85515540-85515690	HEK293	kidney:	n/a	n/a
7	YY1	chr1:85515479-85515793	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr1:85515096-85515808	HEK293	kidney:	n/a	n/a
9	TCF7L2	chr1:85515084-85515782	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
MCOLN3	TF binding region

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443172	0.84[ASN][1000 genomes]
rs12024977	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028736	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037219	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042160	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028304	0.84[ASN][1000 genomes]
rs2304641	0.99[ASN][1000 genomes]
rs2840050	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61768854	0.93[EUR][1000 genomes]
rs61769366	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61770879	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665436	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679539	0.84[ASN][1000 genomes]
rs6688354	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700723	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522239	0.84[ASN][1000 genomes]
rs7540706	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547224	0.89[EUR][1000 genomes]
rs7547317	0.89[EUR][1000 genomes]
rs893618	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898036	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85512400-85515800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:85513000-85515800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:85513000-85515800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:85513200-85515800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr1:85514600-85515800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:85514600-85516200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:85514600-85516600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr1:85514600-85516800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr1:85514600-85517600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:85514800-85515800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr1:85514800-85515800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:85514800-85516400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr1:85514800-85527400	Weak transcription	Aorta	Aorta
14	chr1:85515000-85515800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr1:85515200-85515800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr1:85515200-85515800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr1:85515200-85515800	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr1:85515200-85516200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:85515200-85517600	Enhancers	Dnd41	blood
20	chr1:85515400-85515800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:85515400-85515800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:85515400-85515800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr1:85515400-85515800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr1:85515600-85515800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:85515600-85515800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
26	chr1:85515600-85515800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:85515600-85515800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:85515600-85515800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr1:85515600-85515800	Bivalent Enhancer	Fetal Thymus	thymus
30	chr1:85515600-85515800	Flanking Active TSS	Pancreas	Pancrea
31	chr1:85515600-85515800	Enhancers	GM12878-XiMat	blood
32	chr1:85515600-85516400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
33	chr1:85515600-85517000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:85515600-85517200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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