Variant report

Variant	rs67989853
Chromosome Location	chr2:209055164-209055165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:209054232-209055275	H1-neurons	neurons:	n/a	n/a
2	REST	chr2:209053783-209055326	H1-neurons	neurons:	n/a	n/a
3	TAF1	chr2:209054238-209055229	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:209055151-209055201	HAEpiC	amniotic membrane:	n/a
2	chr2:209055151-209055201	PFSK-1	brain:	n/a
3	chr2:209055151-209055201	AG09309	skin:	n/a
4	chr2:209055151-209055201	HRCEpiC	kidney:	n/a
5	chr2:209055151-209055201	HCPEpiC	choroid plexus:	n/a
6	chr2:209055151-209055201	SK-N-MC	brain:	n/a
7	chr2:209055151-209055201	CMK	blood:	n/a
8	chr2:209055151-209055201	HNPCEpiC	eye:	n/a
9	chr2:209055151-209055201	HEEpiC	esophagus:	n/a
10	chr2:209055151-209055201	GM12892	blood:	n/a
11	chr2:209055151-209055201	Jurkat	blood:	n/a
12	chr2:209055151-209055201	A549	lung:	n/a
13	chr2:209055151-209055201	ProgFib	skin:	n/a
14	chr2:209055151-209055201	BE2_C	brain:	n/a
15	chr2:209055151-209055201	AG04449	skin:	fetal
16	chr2:209055151-209055201	ovcar-3	ovarian:	n/a
17	chr2:209055151-209055201	NT2-D1	testis:	n/a
18	chr2:209055151-209055201	RPTEC	kidney:	n/a
19	chr2:209055151-209055201	T-47D	breast:	n/a
20	chr2:209055151-209055201	AoSMC	blood vessel:	n/a
21	chr2:209055151-209055201	SKMC	muscle:	n/a
22	chr2:209055151-209055201	HEK293	kidney:	embryo
23	chr2:209055151-209055201	NH-A	brain:	n/a
24	chr2:209055151-209055201	SAEC	small airway:	n/a
25	chr2:209055151-209055201	HPAEpiC	pulmonary alveolar:	n/a
26	chr2:209055151-209055201	HCF	heart:	n/a
27	chr2:209055151-209055201	AG04450	lung:	fetal
28	chr2:209055151-209055201	GM12878	blood:	n/a
29	chr2:209055151-209055201	SK-N-SH_RA	brain:	n/a
30	chr2:209055151-209055201	HL-60	blood:	n/a
31	chr2:209055151-209055201	NB4	blood:	n/a
32	chr2:209055151-209055201	BJ	skin:	n/a
33	chr2:209055151-209055201	H1-hESC	embryonic stem cell:	embryo
34	chr2:209055151-209055201	PANC-1	pancreas:	n/a
35	chr2:209055151-209055201	HCT-116	colon:	n/a
36	chr2:209055151-209055201	SK-N-SH	brain:	n/a
37	chr2:209055151-209055201	ECC-1	luminal epithelium:	n/a
38	chr2:209055151-209055201	AG09319	gingival:	n/a
39	chr2:209055151-209055201	NHBE	bronchial:	n/a
40	chr2:209055151-209055201	HRE	kidney:	n/a
41	chr2:209055151-209055201	HRPEpiC	eye:	n/a
42	chr2:209055151-209055201	HCM	heart:	n/a
43	chr2:209055151-209055201	GM19239	blood:	n/a
44	chr2:209055151-209055201	MCF-7	breast:	n/a
45	chr2:209055151-209055201	HepG2	liver:	n/a
46	chr2:209055151-209055201	PrEC	prostate:	n/a
47	chr2:209055151-209055201	HIPEpiC	eye:	n/a
48	chr2:209055151-209055201	LNCaP	prostate:	n/a
49	chr2:209055151-209055201	HUVEC	blood vessel:	n/a
50	chr2:209055151-209055201	GM12891	blood:	n/a

No data

Variant related genes	Relation type
C2orf80	TF binding region
C2orf80	CpG island

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10497896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804167	0.81[ASN][1000 genomes]
rs11676550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883992	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12373582	0.85[AFR][1000 genomes]
rs12986551	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995124	0.81[ASN][1000 genomes]
rs12995271	0.81[ASN][1000 genomes]
rs13020590	0.86[AFR][1000 genomes]
rs13027349	0.86[AFR][1000 genomes]
rs34029379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34575089	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35551278	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705133	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710217	1.00[ASN][1000 genomes]
rs6710543	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725512	1.00[ASN][1000 genomes]
rs6749281	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751157	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs71418664	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71418665	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72974837	0.93[ASN][1000 genomes]
rs7572263	1.00[ASN][1000 genomes]
rs7579275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583625	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv584299	chr2:209021232-209067051	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv875749	chr2:209022909-209062388	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv875750	chr2:209022909-209069303	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv869592	chr2:209029861-209060862	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2763083	chr2:209033581-209058397	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv522180	chr2:209052303-209062388	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv274878	chr2:209054297-209058385	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209040000-209064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:209051200-209055200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:209051800-209055400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:209053400-209056000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:209054200-209055200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:209054200-209055200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:209054200-209055800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:209054400-209055200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:209054400-209056000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:209054800-209055200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:209054800-209055200	Flanking Active TSS	Fetal Brain Female	brain
12	chr2:209054800-209056000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:209054800-209056200	Enhancers	Fetal Brain Male	brain
14	chr2:209055000-209055200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:209055000-209055200	Enhancers	Brain Angular Gyrus	brain
16	chr2:209055000-209055200	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr2:209055000-209056200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:209055000-209061000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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