Variant report

Variant	rs1022486
Chromosome Location	chr6:27534240-27534241
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:27533492-27534336	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:27533677-27534565	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr6:27533651-27534377	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr6:27533601-27534449	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr6:27533639-27534448	A549	lung:	n/a	n/a
6	MAX	chr6:27533644-27534325	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr6:27533429-27534525	A549	lung:	n/a	n/a
8	POLR2A	chr6:27533958-27534313	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr6:27533520-27534306	A549	lung:	n/a	n/a
10	CTBP2	chr6:27533588-27534428	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr6:27533488-27534253	A549	lung:	n/a	n/a
12	SIN3AK20	chr6:27533594-27534374	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr6:27533517-27534268	H1-hESC	embryonic stem cell:	n/a	n/a
14	ATF2	chr6:27533459-27534293	H1-hESC	embryonic stem cell:	n/a	n/a
15	CREB1	chr6:27533432-27534373	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27532532..27534367-chr6:27543877..27545745,2	K562	blood:
2	chr6:27524177..27527153-chr6:27531672..27535728,3	MCF-7	breast:
3	chr6:27532784..27536184-chr6:27537874..27540243,4	K562	blood:
4	chr6:27518662..27523972-chr6:27530343..27535715,8	K562	blood:
5	chr6:27529191..27531638-chr6:27533093..27535191,2	K562	blood:
6	chr6:27532973..27535068-chr6:27541165..27542724,2	K562	blood:
7	chr6:27532266..27536184-chr6:27537870..27540243,4	K562	blood:
8	chr6:27528306..27529946-chr6:27532620..27534637,2	MCF-7	breast:
9	chr6:27532623..27535233-chr6:27560375..27562747,2	K562	blood:
10	chr6:27531650..27535233-chr6:27560375..27562860,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000219738	TF binding region
ENSG00000219738	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10807026	0.97[ASN][1000 genomes]
rs10807029	0.85[ASN][1000 genomes]
rs10946932	0.81[YRI][hapmap]
rs10946935	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs10946938	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946940	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12197514	0.86[ASN][1000 genomes]
rs2056924	0.91[JPT][hapmap]
rs2294308	0.82[YRI][hapmap]
rs2294309	0.82[YRI][hapmap]
rs2294480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2294481	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4272217	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4478400	0.85[YRI][hapmap]
rs4713112	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4713113	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713120	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs62401383	0.90[ASN][1000 genomes]
rs6456799	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs67734963	0.92[ASN][1000 genomes]
rs6908295	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6914981	0.84[ASN][1000 genomes]
rs6915266	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6915987	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6916878	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6918038	0.85[ASN][1000 genomes]
rs6921256	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6933926	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6934437	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6934794	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7769662	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7774613	0.85[YRI][hapmap]
rs7774939	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775817	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348772	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs9357042	0.82[ASN][1000 genomes]
rs9380007	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs9393830	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9393831	0.93[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs9468141	0.82[YRI][hapmap]
rs9468156	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27532000-27535800	Weak transcription	K562	blood
2	chr6:27533200-27534800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:27533200-27534800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27533400-27534400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27533400-27534600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:27533400-27534600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:27533400-27534600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:27533400-27534800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr6:27533400-27534800	Active TSS	A549	lung
10	chr6:27533600-27534400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:27533600-27534400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:27533600-27534400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:27533600-27534400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:27533600-27534400	Flanking Active TSS	HMEC	breast
15	chr6:27533600-27534600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr6:27533600-27534800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:27533600-27535000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:27533800-27534400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:27533800-27534400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr6:27533800-27534400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:27533800-27534400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:27533800-27534400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr6:27533800-27534400	Enhancers	Pancreas	Pancrea
26	chr6:27533800-27534400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr6:27533800-27534800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr6:27533800-27535000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:27534000-27534400	Flanking Bivalent TSS/Enh	Placenta	Placenta
30	chr6:27534000-27534400	Bivalent/Poised TSS	HepG2	liver
31	chr6:27534200-27534400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:27534200-27534400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:27534200-27534400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:27534200-27534400	Bivalent Enhancer	Fetal Intestine Large	intestine
35	chr6:27534200-27534600	Active TSS	GM12878-XiMat	blood
36	chr6:27534200-27534600	Bivalent/Poised TSS	NHEK	skin

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