Variant report

Variant	rs10480492
Chromosome Location	chr7:129007820-129007821
allele	C/T
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	POU2F2	chr7:129007804-129008773	GM12878	blood:	n/a	n/a
2	MTA3	chr7:129007387-129008814	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:129007456-129008381	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr7:129007412-129008055	GM12878	blood:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
5	WRNIP1	chr7:129007304-129008901	GM12878	blood:	n/a	n/a
6	TCF7L2	chr7:129007566-129008219	HEK293	kidney:	n/a	chr7:129007781-129007795
7	POLR2A	chr7:129007790-129008785	GM12892	blood:	n/a	n/a
8	EP300	chr7:129007659-129008209	Hela-S3	cervix:	n/a	chr7:129007966-129007975
9	MAZ	chr7:129007405-129008146	Hela-S3	cervix:	n/a	chr7:129008084-129008093
10	TBL1XR1	chr7:129007540-129009184	GM12878	blood:	n/a	n/a
11	RAD21	chr7:129007234-129008155	HCT-116	colon:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
12	ZNF143	chr7:129007409-129008888	GM12878	blood:	n/a	n/a
13	RAD21	chr7:129007272-129007995	HCT-116	colon:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
14	TEAD4	chr7:129007336-129008372	K562	blood:	n/a	n/a
15	CTCF	chr7:129007175-129008019	HCT-116	colon:	n/a	chr7:129007600-129007621 chr7:129007601-129007614 chr7:129007598-129007616 chr7:129007599-129007615
16	EP300	chr7:129007420-129007942	K562	blood:	n/a	n/a
17	BHLHE40	chr7:129007438-129008877	GM12878	blood:	n/a	n/a
18	FOXA1	chr7:129007618-129008021	T-47D	breast:	n/a	chr7:129007819-129007834
19	RAD21	chr7:129007281-129007917	H1-hESC	embryonic stem cell:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
20	CUX1	chr7:129007388-129008139	K562	blood:	n/a	n/a
21	FOXP2	chr7:129007666-129008072	SK-N-MC	brain:	n/a	n/a
22	CHD1	chr7:129007459-129008947	GM12878	blood:	n/a	n/a
23	ATF1	chr7:129007442-129008228	K562	blood:	n/a	chr7:129007909-129007923
24	GATA3	chr7:129007415-129007971	T-47D	breast:	n/a	n/a
25	ZNF217	chr7:129007532-129007974	MCF-7	breast:	n/a	n/a
26	CTCF	chr7:129007382-129007918	HCT-116	colon:	n/a	chr7:129007600-129007621 chr7:129007601-129007614 chr7:129007598-129007616 chr7:129007599-129007615
27	SPI1	chr7:129007757-129008855	GM12878	blood:	n/a	n/a
28	CHD2	chr7:129007584-129008029	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr7:129007392-129007840	GM12878	blood:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
30	RELA	chr7:129007408-129008883	GM12891	blood:	n/a	chr7:129008642-129008651 chr7:129008642-129008651
31	CTCF	chr7:129007266-129007946	K562	blood:	n/a	chr7:129007600-129007621 chr7:129007601-129007614 chr7:129007598-129007616 chr7:129007599-129007615
32	TFAP2C	chr7:129007275-129008225	Hela-S3	cervix:	n/a	chr7:129007566-129007581
33	STAT3	chr7:129007618-129008241	Hela-S3	cervix:	n/a	chr7:129007969-129007976
34	ATF2	chr7:129007347-129008950	GM12878	blood:	n/a	chr7:129007909-129007923
35	EP300	chr7:129007438-129008981	GM12878	blood:	n/a	chr7:129008697-129008711 chr7:129007966-129007975
36	RAD21	chr7:129007290-129007827	H1-hESC	embryonic stem cell:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
37	USF2	chr7:129007670-129008008	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr7:129007396-129008270	K562	blood:	n/a	n/a
39	CEBPB	chr7:129007429-129008376	Hela-S3	cervix:	n/a	n/a
40	TCF7L2	chr7:129007521-129008348	Hela-S3	cervix:	n/a	chr7:129007781-129007795
41	POLR2A	chr7:129007433-129008342	U87	brain:	n/a	n/a
42	RELA	chr7:129007466-129008919	GM10847	blood:	n/a	chr7:129008642-129008651 chr7:129008642-129008651
43	RCOR1	chr7:129007429-129008921	GM12878	blood:	n/a	n/a
44	RAD21	chr7:129007355-129007882	ECC-1	luminal epithelium:	n/a	chr7:129007599-129007618 chr7:129007600-129007614
45	STAT5A	chr7:129007315-129008370	GM12878	blood:	n/a	chr7:129007969-129007976 chr7:129008279-129008286
46	BCLAF1	chr7:129007366-129008885	GM12878	blood:	n/a	chr7:129007609-129007617
47	CTCF	chr7:129007325-129007900	MCF-7	breast:	n/a	chr7:129007600-129007621 chr7:129007601-129007614 chr7:129007598-129007616 chr7:129007599-129007615
48	CTCF	chr7:129007375-129007825	K562	blood:	n/a	chr7:129007600-129007621 chr7:129007601-129007614 chr7:129007598-129007616 chr7:129007599-129007615
49	CUX1	chr7:129007310-129008222	GM12878	blood:	n/a	n/a
50	CTCF	chr7:129007800-129007950	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:129007148..129007884-chr7:129650404..129650911,2	K562	blood:
2	chr7:129006160..129011107-chr7:129012135..129016700,5	K562	blood:
3	chr7:129007269..129007980-chr7:129073745..129074746,3	MCF-7	breast:
4	chr7:129007192..129007924-chr7:129016118..129016695,2	K562	blood:
5	chr7:129007427..129007933-chr7:129110880..129111628,2	MCF-7	breast:

Variant related genes	Relation type
AHCYL2	TF binding region
ENSG00000158467	Chromatin interaction
ENSG00000128578	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10264209	1.00[EUR][1000 genomes]
rs1248453	1.00[EUR][1000 genomes]
rs2052962	1.00[EUR][1000 genomes]
rs2703098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718109	1.00[EUR][1000 genomes]
rs28437865	1.00[EUR][1000 genomes]
rs28475451	1.00[EUR][1000 genomes]
rs682299	1.00[EUR][1000 genomes]
rs7805353	1.00[EUR][1000 genomes]
rs9649526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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
6	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS 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

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128989200-129044200	Weak transcription	Ovary	ovary
2	chr7:128999600-129008000	Weak transcription	Small Intestine	intestine
3	chr7:129006200-129046000	Weak transcription	Aorta	Aorta
4	chr7:129006800-129008000	Enhancers	Stomach Mucosa	stomach
5	chr7:129007200-129008000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:129007200-129008200	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr7:129007200-129008200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:129007200-129008400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:129007200-129008400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr7:129007200-129008600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:129007200-129008600	Enhancers	Fetal Heart	heart
12	chr7:129007200-129008800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr7:129007200-129008800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:129007200-129009000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:129007200-129009000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:129007200-129011400	Active TSS	Rectal Smooth Muscle	rectum
17	chr7:129007400-129008000	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:129007400-129008000	Enhancers	Stomach Smooth Muscle	stomach
19	chr7:129007400-129008200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:129007400-129008200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:129007400-129008400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr7:129007400-129008400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:129007400-129008400	Enhancers	Brain Angular Gyrus	brain
24	chr7:129007400-129008400	Enhancers	Brain Germinal Matrix	brain
25	chr7:129007400-129008400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr7:129007400-129008600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:129007400-129008600	Enhancers	Pancreas	Pancrea
28	chr7:129007400-129008800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:129007400-129008800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr7:129007400-129008800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:129007400-129008800	Enhancers	Fetal Lung	lung
32	chr7:129007400-129008800	Enhancers	Placenta	Placenta
33	chr7:129007400-129008800	Flanking Active TSS	GM12878-XiMat	blood
34	chr7:129007400-129008800	Flanking Active TSS	Hela-S3	cervix
35	chr7:129007600-129008000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:129007600-129008000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr7:129007600-129008000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr7:129007600-129008000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr7:129007600-129008000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr7:129007600-129008000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr7:129007600-129008000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr7:129007600-129008000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr7:129007600-129008000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:129007600-129008000	Flanking Active TSS	A549	lung
45	chr7:129007600-129008000	Flanking Active TSS	K562	blood
46	chr7:129007600-129008000	Active TSS	NHDF-Ad	bronchial
47	chr7:129007600-129008000	Enhancers	NHEK	skin
48	chr7:129007600-129008200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:129007600-129008200	Enhancers	Primary hematopoietic stem cells	blood
50	chr7:129007600-129008200	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links