Variant report

Variant	rs793656
Chromosome Location	chr6:24402752-24402753
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	MAX	chr6:24402713-24404074	HepG2	liver:	n/a	n/a
2	MAFK	chr6:24402649-24403438	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr6:24402643-24403772	Hela-S3	cervix:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
4	POLR2A	chr6:24402715-24403861	PFSK-1	brain:	n/a	n/a
5	MXI1	chr6:24402580-24404065	IMR90	lung:	n/a	n/a
6	POLR2A	chr6:24402710-24403983	SK-N-MC	brain:	n/a	n/a
7	CHD1	chr6:24402666-24403634	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr6:24402723-24403242	ECC-1	luminal epithelium:	n/a	n/a
9	ZEB1	chr6:24402209-24403982	HepG2	liver:	n/a	chr6:24403031-24403042
10	HCFC1	chr6:24402667-24404146	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr6:24402531-24402833	HepG2	liver:	n/a	n/a
12	REST	chr6:24402707-24403266	MCF-7	breast:	n/a	n/a
13	REST	chr6:24402733-24403756	H1-neurons	neurons:	n/a	chr6:24403613-24403626
14	MAX	chr6:24402733-24403692	MCF-7	breast:	n/a	n/a
15	ZEB1	chr6:24402318-24404205	HepG2	liver:	n/a	chr6:24403031-24403042
16	BRCA1	chr6:24402721-24403465	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr6:24402749-24403563	HUVEC	blood vessel:	n/a	n/a
18	REST	chr6:24402729-24403503	MCF-7	breast:	n/a	n/a
19	POLR2A	chr6:24401543-24404415	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:

Variant related genes	Relation type
MRS2	TF binding region
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1277345	0.84[AFR][1000 genomes]
rs1772256	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2744549	1.00[CHD][hapmap]
rs2744550	1.00[CHD][hapmap]
rs2744559	1.00[CHD][hapmap]
rs2817191	1.00[CHD][hapmap]
rs2817195	1.00[CHD][hapmap]
rs4418171	0.82[AFR][1000 genomes]
rs4472344	1.00[CHD][hapmap]
rs6941710	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7744621	1.00[CHD][hapmap]
rs7744939	1.00[CHD][hapmap]
rs7749794	1.00[CHD][hapmap]
rs7751846	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs7752186	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs7752603	1.00[CEU][hapmap];1.00[CHD][hapmap];0.80[YRI][hapmap]
rs7757601	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7760171	1.00[CHD][hapmap]
rs7764860	1.00[CHD][hapmap]
rs7768124	1.00[CEU][hapmap]
rs7770041	1.00[CHD][hapmap]
rs7772115	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs7772540	1.00[CEU][hapmap];1.00[CHD][hapmap];0.80[YRI][hapmap]
rs9467136	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs9467139	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9467151	1.00[CEU][hapmap]
rs9467152	1.00[CEU][hapmap]
rs9467154	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24400200-24402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:24400600-24402800	Enhancers	K562	blood
3	chr6:24401000-24402800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:24401200-24402800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:24401200-24402800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:24401200-24402800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:24401200-24402800	Enhancers	Fetal Intestine Large	intestine
8	chr6:24401200-24402800	Enhancers	Placenta	Placenta
9	chr6:24401200-24403000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr6:24401200-24403000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:24401800-24402800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:24401800-24403000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:24402000-24402800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:24402000-24402800	Enhancers	Fetal Heart	heart
16	chr6:24402000-24402800	Weak transcription	Psoas Muscle	Psoas
17	chr6:24402000-24403000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:24402200-24403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:24402400-24402800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:24402400-24402800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:24402400-24402800	Enhancers	Brain Hippocampus Middle	brain
22	chr6:24402400-24402800	Enhancers	Colon Smooth Muscle	Colon
23	chr6:24402400-24402800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr6:24402400-24402800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:24402400-24402800	Enhancers	Thymus	Thymus
26	chr6:24402400-24402800	Flanking Active TSS	HepG2	liver
27	chr6:24402400-24402800	Enhancers	NHEK	skin
28	chr6:24402400-24403000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:24402400-24403000	Flanking Active TSS	Fetal Lung	lung
30	chr6:24402400-24403200	Active TSS	Brain Germinal Matrix	brain
31	chr6:24402400-24403200	Flanking Active TSS	Dnd41	blood
32	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:24402600-24402800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:24402600-24402800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:24402600-24402800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:24402600-24402800	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:24402600-24402800	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:24402600-24402800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr6:24402600-24402800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:24402600-24402800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:24402600-24402800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:24402600-24402800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:24402600-24402800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:24402600-24402800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:24402600-24402800	Enhancers	Colonic Mucosa	Colon
46	chr6:24402600-24402800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:24402600-24402800	Flanking Active TSS	Fetal Brain Female	brain
48	chr6:24402600-24402800	Enhancers	Fetal Intestine Small	intestine
49	chr6:24402600-24402800	Active TSS	Fetal Muscle Trunk	muscle
50	chr6:24402600-24402800	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links