Variant report

Variant	rs542418472
Chromosome Location	chr6:24494643-24494644
allele	A/G
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:9)
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	CTCF	chr6:24494560-24494710	GM12870	blood:	n/a	n/a
2	CTCF	chr6:24494347-24496072	SK-N-SH	brain:	n/a	n/a
3	TEAD4	chr6:24494607-24495256	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr6:24494549-24496168	K562	blood:	n/a	n/a
5	GABPA	chr6:24494560-24495467	K562	blood:	n/a	chr6:24495173-24495187
6	POLR2A	chr6:24494608-24496269	HepG2	liver:	n/a	n/a
7	MAX	chr6:24494592-24496234	HepG2	liver:	n/a	chr6:24495932-24495942
8	REST	chr6:24494454-24495983	H1-neurons	neurons:	n/a	chr6:24495026-24495039
9	CTCF	chr6:24494600-24494750	GM12873	blood:	n/a	n/a
10	GATA1	chr6:24493258-24495592	PBDE	blood:	n/a	n/a
11	HDAC2	chr6:24494626-24496196	HepG2	liver:	n/a	chr6:24495176-24495185 chr6:24496097-24496111
12	MAX	chr6:24494452-24496224	HepG2	liver:	n/a	chr6:24495932-24495942
13	CREB1	chr6:24494495-24496123	HepG2	liver:	n/a	n/a
14	TEAD4	chr6:24494605-24495034	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZEB1	chr6:24494635-24495122	GM12878	blood:	n/a	n/a
16	BHLHE40	chr6:24494635-24496143	K562	blood:	n/a	n/a
17	MXI1	chr6:24494625-24496091	HepG2	liver:	n/a	n/a
18	SETDB1	chr6:24494597-24496206	K562	blood:	n/a	chr6:24495177-24495186
19	UBTF	chr6:24494398-24496033	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:24494605-24494655	SK-N-MC	brain:	n/a
2	chr6:24494605-24494655	AoSMC	blood vessel:	n/a
3	chr6:24494605-24494655	CMK	blood:	n/a
4	chr6:24494605-24494655	SK-N-SH	brain:	n/a
5	chr6:24494605-24494655	T-47D	breast:	n/a
6	chr6:24494605-24494655	BE2_C	brain:	n/a
7	chr6:24494605-24494655	LNCaP	prostate:	n/a
8	chr6:24494605-24494655	H1-hESC	embryonic stem cell:	embryo
9	chr6:24494605-24494655	ProgFib	skin:	n/a
10	chr6:24494605-24494655	AG09319	gingival:	n/a
11	chr6:24494605-24494655	PFSK-1	brain:	n/a
12	chr6:24494605-24494655	ovcar-3	ovarian:	n/a
13	chr6:24494605-24494655	HCPEpiC	choroid plexus:	n/a
14	chr6:24494605-24494655	NHDF-neo	bronchial:	n/a
15	chr6:24494605-24494655	PrEC	prostate:	n/a
16	chr6:24494605-24494655	HEEpiC	esophagus:	n/a
17	chr6:24494605-24494655	SAEC	small airway:	n/a
18	chr6:24494605-24494655	HRE	kidney:	n/a
19	chr6:24494605-24494655	HCF	heart:	n/a
20	chr6:24494605-24494655	HIPEpiC	eye:	n/a
21	chr6:24494605-24494655	SK-N-SH_RA	brain:	n/a
22	chr6:24494605-24494655	HUVEC	blood vessel:	n/a
23	chr6:24494605-24494655	HepG2	liver:	n/a
24	chr6:24494605-24494655	HL-60	blood:	n/a
25	chr6:24494605-24494655	MCF-7	breast:	n/a
26	chr6:24494605-24494655	NHBE	bronchial:	n/a
27	chr6:24494605-24494655	SKMC	muscle:	n/a
28	chr6:24494605-24494655	NT2-D1	testis:	n/a
29	chr6:24494605-24494655	HNPCEpiC	eye:	n/a
30	chr6:24494605-24494655	A549	lung:	n/a
31	chr6:24494605-24494655	HRPEpiC	eye:	n/a
32	chr6:24494605-24494655	Caco-2	colon:	n/a
33	chr6:24494605-24494655	GM19239	blood:	n/a
34	chr6:24494605-24494655	AG04450	lung:	fetal
35	chr6:24494605-24494655	GM06990	blood:	n/a
36	chr6:24494605-24494655	GM12878	blood:	n/a
37	chr6:24494605-24494655	Jurkat	blood:	n/a
38	chr6:24494605-24494655	BJ	skin:	n/a
39	chr6:24494605-24494655	NH-A	brain:	n/a
40	chr6:24494605-24494655	Hela-S3	cervix:	n/a
41	chr6:24494605-24494655	HEK293	kidney:	embryo
42	chr6:24494605-24494655	HCT-116	colon:	n/a
43	chr6:24494605-24494655	RPTEC	kidney:	n/a
44	chr6:24494605-24494655	AG04449	skin:	fetal
45	chr6:24494605-24494655	K562	blood:	n/a
46	chr6:24494605-24494655	PANC-1	pancreas:	n/a
47	chr6:24494605-24494655	AG10803	skin:	n/a
48	chr6:24494605-24494655	U87	brain:	n/a
49	chr6:24494605-24494655	GM12892	blood:	n/a
50	chr6:24494605-24494655	HMEC	breast:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
2	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
3	chr6:24492199..24495699-chr6:24718792..24721987,5	K562	blood:
4	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:
5	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
6	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
7	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
8	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
9	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:

No data

Variant related genes	Relation type
ALDH5A1	TF binding region
GPLD1	TF binding region
ALDH5A1	CpG island
GPLD1	CpG island
ENSG00000112312	Chromatin interaction
ENSG00000124532	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3351586	chr6:24494123-24497171	Bivalent/Poised TSS Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24493200-24495000	Flanking Active TSS	K562	blood
2	chr6:24493800-24494800	Flanking Active TSS	Dnd41	blood
3	chr6:24494000-24495000	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr6:24494000-24495000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:24494000-24496000	Active TSS	Brain Angular Gyrus	brain
6	chr6:24494000-24496000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:24494200-24494800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
8	chr6:24494200-24494800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr6:24494200-24494800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr6:24494200-24494800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr6:24494200-24494800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr6:24494200-24494800	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr6:24494200-24494800	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr6:24494200-24494800	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:24494200-24495000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:24494200-24495000	Flanking Active TSS	HepG2	liver
17	chr6:24494200-24495200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr6:24494400-24494800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:24494400-24494800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr6:24494400-24494800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:24494400-24494800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:24494400-24494800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:24494400-24494800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr6:24494400-24494800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr6:24494400-24494800	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr6:24494400-24494800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:24494400-24494800	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr6:24494400-24494800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr6:24494400-24494800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
30	chr6:24494400-24494800	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr6:24494400-24494800	Enhancers	Spleen	Spleen
32	chr6:24494400-24494800	Enhancers	HUVEC	blood vessel
33	chr6:24494400-24495000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr6:24494400-24495000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:24494400-24495000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr6:24494400-24495000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:24494400-24495000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:24494400-24495000	Flanking Active TSS	Liver	Liver
39	chr6:24494400-24495000	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr6:24494400-24495000	Flanking Active TSS	Fetal Thymus	thymus
41	chr6:24494400-24495000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr6:24494400-24495000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr6:24494400-24495000	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr6:24494400-24495000	Flanking Active TSS	Thymus	Thymus
45	chr6:24494400-24495000	Flanking Active TSS	Hela-S3	cervix
46	chr6:24494400-24495200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr6:24494400-24495200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr6:24494400-24495200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:24494400-24495200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:24494400-24495600	Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links