Variant report

Variant	rs12209038
Chromosome Location	chr6:27534185-27534186
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 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	ELF1	chr6:27533760-27534225	GM12878	blood:	n/a	n/a
4	MXI1	chr6:27533651-27534377	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr6:27533601-27534449	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr6:27533639-27534448	A549	lung:	n/a	n/a
7	CREB1	chr6:27533670-27534235	A549	lung:	n/a	n/a
8	MAX	chr6:27533644-27534325	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr6:27533429-27534525	A549	lung:	n/a	n/a
10	POLR2A	chr6:27533958-27534313	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr6:27533520-27534306	A549	lung:	n/a	n/a
12	CTBP2	chr6:27533588-27534428	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr6:27533488-27534253	A549	lung:	n/a	n/a
14	CREB1	chr6:27533480-27534224	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr6:27533594-27534374	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:27534081-27534189	MCF-7	breast:	n/a	n/a
17	CREB1	chr6:27533517-27534268	H1-hESC	embryonic stem cell:	n/a	n/a
18	ATF2	chr6:27533459-27534293	H1-hESC	embryonic stem cell:	n/a	n/a
19	CREB1	chr6:27533432-27534373	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27534137-27534187	NT2-D1	testis:	n/a
2	chr6:27534137-27534187	HRCEpiC	kidney:	n/a
3	chr6:27534137-27534187	GM06990	blood:	n/a
4	chr6:27534137-27534187	BJ	skin:	n/a
5	chr6:27534137-27534187	HRPEpiC	eye:	n/a
6	chr6:27534137-27534187	HEK293	kidney:	embryo
7	chr6:27534137-27534187	HAEpiC	amniotic membrane:	n/a
8	chr6:27534137-27534187	NH-A	brain:	n/a
9	chr6:27534137-27534187	Jurkat	blood:	n/a
10	chr6:27534137-27534187	HCT-116	colon:	n/a
11	chr6:27534137-27534187	HL-60	blood:	n/a
12	chr6:27534137-27534187	K562	blood:	n/a
13	chr6:27534137-27534187	ProgFib	skin:	n/a
14	chr6:27534137-27534187	BE2_C	brain:	n/a
15	chr6:27534137-27534187	IMR90	lung:	fetal
16	chr6:27534137-27534187	PANC-1	pancreas:	n/a
17	chr6:27534137-27534187	CMK	blood:	n/a
18	chr6:27534137-27534187	AG09309	skin:	n/a
19	chr6:27534137-27534187	GM19239	blood:	n/a
20	chr6:27534137-27534187	HCPEpiC	choroid plexus:	n/a
21	chr6:27534137-27534187	SKMC	muscle:	n/a
22	chr6:27534137-27534187	ovcar-3	ovarian:	n/a
23	chr6:27534137-27534187	H1-hESC	embryonic stem cell:	embryo
24	chr6:27534137-27534187	LNCaP	prostate:	n/a
25	chr6:27534137-27534187	AG09319	gingival:	n/a
26	chr6:27534137-27534187	SK-N-MC	brain:	n/a
27	chr6:27534137-27534187	HRE	kidney:	n/a
28	chr6:27534137-27534187	Hela-S3	cervix:	n/a
29	chr6:27534137-27534187	MCF10A-Er-Src	breast:	n/a
30	chr6:27534137-27534187	U87	brain:	n/a
31	chr6:27534137-27534187	HEEpiC	esophagus:	n/a
32	chr6:27534137-27534187	SK-N-SH	brain:	n/a
33	chr6:27534137-27534187	NHDF-neo	bronchial:	n/a
34	chr6:27534137-27534187	SK-N-SH_RA	brain:	n/a
35	chr6:27534137-27534187	A549	lung:	n/a
36	chr6:27534137-27534187	NB4	blood:	n/a
37	chr6:27534137-27534187	GM12891	blood:	n/a
38	chr6:27534137-27534187	HUVEC	blood vessel:	n/a
39	chr6:27534137-27534187	RPTEC	kidney:	n/a
40	chr6:27534137-27534187	ECC-1	luminal epithelium:	n/a
41	chr6:27534137-27534187	HCF	heart:	n/a
42	chr6:27534137-27534187	PrEC	prostate:	n/a
43	chr6:27534137-27534187	AG04449	skin:	fetal
44	chr6:27534137-27534187	HIPEpiC	eye:	n/a
45	chr6:27534137-27534187	HNPCEpiC	eye:	n/a
46	chr6:27534137-27534187	HCM	heart:	n/a
47	chr6:27534137-27534187	HMEC	breast:	n/a
48	chr6:27534137-27534187	PFSK-1	brain:	n/a
49	chr6:27534137-27534187	AG04450	lung:	fetal
50	chr6:27534137-27534187	AoSMC	blood vessel:	n/a

(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	CpG island
ENSG00000219738	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10456356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211424	1.00[ASN][1000 genomes]
rs12212404	1.00[ASN][1000 genomes]
rs12213302	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393997	1.00[ASN][1000 genomes]
rs4711160	1.00[ASN][1000 genomes]
rs4713091	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs645666	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6456787	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6930169	1.00[ASN][1000 genomes]
rs7748123	1.00[ASN][1000 genomes]
rs7756309	1.00[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:40 , 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	chr6:27533400-27534200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:27533400-27534200	Flanking Bivalent TSS/Enh	NHEK	skin
6	chr6:27533400-27534400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:27533400-27534600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:27533400-27534600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:27533400-27534600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:27533400-27534800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:27533400-27534800	Active TSS	A549	lung
12	chr6:27533600-27534200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr6:27533600-27534200	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:27533600-27534400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:27533600-27534400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:27533600-27534400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:27533600-27534400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:27533600-27534400	Flanking Active TSS	HMEC	breast
19	chr6:27533600-27534600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr6:27533600-27534800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:27533600-27535000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:27533800-27534400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:27533800-27534400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
26	chr6:27533800-27534400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:27533800-27534400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:27533800-27534400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr6:27533800-27534400	Enhancers	Pancreas	Pancrea
30	chr6:27533800-27534400	Active TSS	Placenta Amnion	Placenta Amnion
31	chr6:27533800-27534800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:27533800-27535000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr6:27534000-27534200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
34	chr6:27534000-27534200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr6:27534000-27534200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr6:27534000-27534200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr6:27534000-27534200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr6:27534000-27534200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:27534000-27534400	Flanking Bivalent TSS/Enh	Placenta	Placenta
40	chr6:27534000-27534400	Bivalent/Poised TSS	HepG2	liver

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