Variant report

Variant	rs2518723
Chromosome Location	chr9:21995882-21995883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:169)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:169 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:21995800-21995950	HPF	lung:	n/a	n/a
2	RAD21	chr9:21994704-21995967	IMR90	lung:	n/a	n/a
3	CTCF	chr9:21995740-21995890	BJ	skin:	n/a	n/a
4	CTCF	chr9:21995800-21995950	HCT-116	colon:	n/a	n/a
5	CTCF	chr9:21995800-21995950	HPAF	blood vessel:	n/a	n/a
6	POLR2A	chr9:21994926-21996113	PFSK-1	brain:	n/a	n/a
7	SIN3AK20	chr9:21995219-21995909	PFSK-1	brain:	n/a	n/a
8	CTCF	chr9:21995742-21995986	Spleen_OC	spleen:	n/a	n/a
9	GTF2F1	chr9:21995854-21996669	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr9:21995740-21995890	WI-38	lung:	n/a	n/a
11	POLR2A	chr9:21993892-21996090	GM19193	blood:	n/a	n/a
12	E2F6	chr9:21994538-21996627	H1-hESC	embryonic stem cell:	n/a	chr9:21994670-21994677 chr9:21994669-21994681 chr9:21994670-21994677 chr9:21995794-21995806 chr9:21994670-21994677
13	CTCF	chr9:21995760-21995910	GM12864	blood:	n/a	n/a
14	CTCF	chr9:21995760-21995910	AG09309	skin:	n/a	n/a
15	CTCF	chr9:21995760-21995910	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr9:21995820-21995970	BJ	skin:	n/a	n/a
17	POLR2A	chr9:21993809-21996161	IMR90	lung:	n/a	n/a
18	CTCF	chr9:21995800-21995950	GM12869	blood:	n/a	n/a
19	CTCF	chr9:21995760-21995910	GM12875	blood:	n/a	n/a
20	CTCF	chr9:21995820-21995970	Caco-2	colon:	n/a	n/a
21	CTCF	chr9:21995840-21995990	GM12875	blood:	n/a	n/a
22	PAX5	chr9:21995633-21996065	GM12892	blood:	n/a	n/a
23	CTCF	chr9:21995713-21995959	GM19239	blood:	n/a	n/a
24	POLR2A	chr9:21994101-21997363	HEK293	kidney:	n/a	n/a
25	POLR2A	chr9:21992900-21997295	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr9:21993295-21996336	HL-60	blood:	n/a	n/a
27	CTCF	chr9:21995726-21995927	GM13977	blood:	n/a	n/a
28	CTCF	chr9:21995760-21995910	HCM	heart:	n/a	n/a
29	POLR2A	chr9:21995766-21995916	ProgFib	skin:	n/a	n/a
30	CTCF	chr9:21995780-21995930	WERI-Rb-1	eye:	n/a	n/a
31	CTCF	chr9:21995800-21995950	SAEC	small airway:	n/a	n/a
32	CTCF	chr9:21995696-21995905	T-47D	breast:	n/a	n/a
33	CTCF	chr9:21995780-21995930	AG04450	lung:	n/a	n/a
34	CTCF	chr9:21995760-21995910	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr9:21993952-21996245	GM18951	blood:	n/a	n/a
36	RFX5	chr9:21993205-21996658	Hela-S3	cervix:	n/a	chr9:21995409-21995424 chr9:21995409-21995424 chr9:21995409-21995424
37	CTCF	chr9:21995780-21995930	GM12873	blood:	n/a	n/a
38	CTCF	chr9:21995638-21996039	IMR90	lung:	n/a	n/a
39	CTCF	chr9:21995880-21996030	GM12872	blood:	n/a	n/a
40	CTCF	chr9:21995820-21995970	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr9:21995800-21995950	HRPEpiC	eye:	n/a	n/a
42	CTCF	chr9:21995840-21995990	HBMEC	blood vessel:	n/a	n/a
43	TCF12	chr9:21994515-21996219	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr9:21995738-21995937	NHEK	skin:	n/a	n/a
45	POLR2A	chr9:21995710-21996038	HUVEC	blood vessel:	n/a	n/a
46	MAZ	chr9:21993697-21996161	IMR90	lung:	n/a	n/a
47	CTCF	chr9:21995740-21995890	SAEC	small airway:	n/a	n/a
48	SUZ12	chr9:21994805-21996283	H1-hESC	embryonic stem cell:	n/a	n/a
49	E2F6	chr9:21995526-21996530	H1-hESC	embryonic stem cell:	n/a	chr9:21995794-21995806
50	RCOR1	chr9:21993506-21996650	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:21802179..21803949-chr9:21994356..21995893,2	MCF-7	breast:
2	chr9:21995575..21999159-chr9:22007136..22010675,4	MCF-7	breast:
3	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
4	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf53-1	chr9:21995602-21996012	ENSG00000266446.1

No data

Variant related genes	Relation type
CDKN2A	TF binding region
ENSG00000229298	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10115049	0.82[AMR][1000 genomes]
rs10965215	0.82[AMR][1000 genomes]
rs2151280	0.81[AMR][1000 genomes]
rs3218012	0.95[ASN][1000 genomes]
rs496892	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs504318	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs567453	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs643319	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3492902	chr9:21971026-22006145	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3492901	chr9:21971095-22006263	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21992000-21996400	Active TSS	Dnd41	blood
2	chr9:21992800-21996000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:21992800-21996200	Active TSS	Hela-S3	cervix
4	chr9:21993000-21996000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:21993000-21996200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:21993200-21996400	Active TSS	NHDF-Ad	bronchial
7	chr9:21993400-21996000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:21993400-21996000	Active TSS	HSMMtube	muscle
9	chr9:21993400-21996600	Active TSS	NHLF	lung
10	chr9:21993400-21996800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:21993400-21997000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr9:21993600-21996200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr9:21993600-21996200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr9:21993600-21996200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:21993600-21996400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:21993600-21996400	Active TSS	HSMM	muscle
17	chr9:21993600-21996600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:21993600-21996800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr9:21993800-21996200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr9:21993800-21996200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:21993800-21996400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:21993800-21996800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:21994000-21996000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr9:21994000-21996000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr9:21994000-21996000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:21994000-21996000	Active TSS	Brain Substantia Nigra	brain
27	chr9:21994000-21996000	Active TSS	Esophagus	oesophagus
28	chr9:21994000-21996000	Active TSS	Gastric	stomach
29	chr9:21994000-21996000	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr9:21994000-21996200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:21994000-21996400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr9:21994000-21996800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr9:21994200-21996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:21994200-21996000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:21994200-21996000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:21994200-21996000	Active TSS	Brain Angular Gyrus	brain
37	chr9:21994200-21996000	Active TSS	Psoas Muscle	Psoas
38	chr9:21994200-21996000	Active TSS	Small Intestine	intestine
39	chr9:21994200-21996000	Bivalent/Poised TSS	HepG2	liver
40	chr9:21994200-21996200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:21994200-21996200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr9:21994200-21996200	Active TSS	Brain Anterior Caudate	brain
43	chr9:21994200-21996200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr9:21994400-21996000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr9:21994400-21996000	Active TSS	Colon Smooth Muscle	Colon
46	chr9:21994400-21996000	Active TSS	Duodenum Mucosa	Duodenum
47	chr9:21994400-21996000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr9:21994400-21996000	Active TSS	Ovary	ovary
49	chr9:21994400-21996000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr9:21994400-21996000	Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links