Variant report

Variant	rs73070962
Chromosome Location	chr2:209119894-209119895
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	USF1	chr2:209119881-209120106	HepG2	liver:	n/a	n/a
2	FOXP2	chr2:209119786-209120301	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr2:209118794-209120329	GM19193	blood:	n/a	n/a
4	HNF4G	chr2:209119565-209120356	HepG2	liver:	n/a	n/a
5	YY1	chr2:209119568-209120634	SK-N-SH	brain:	n/a	chr2:209119879-209119888
6	MXI1	chr2:209118476-209120613	HepG2	liver:	n/a	n/a
7	YY1	chr2:209119646-209120432	ECC-1	luminal epithelium:	n/a	chr2:209119879-209119888
8	BHLHE40	chr2:209118758-209120311	GM12878	blood:	n/a	n/a
9	EGR1	chr2:209119776-209120067	K562	blood:	n/a	chr2:209119850-209119860 chr2:209119878-209119888 chr2:209119880-209119893
10	POLR2A	chr2:209118690-209120631	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:209119876-209120145	K562	blood:	n/a	n/a
12	POLR2A	chr2:209118607-209120327	K562	blood:	n/a	n/a
13	MTA3	chr2:209118992-209120722	GM12878	blood:	n/a	n/a
14	ZEB1	chr2:209118966-209120238	GM12878	blood:	n/a	n/a
15	IRF1	chr2:209119615-209120302	K562	blood:	n/a	chr2:209119847-209119861 chr2:209119943-209119957 chr2:209119875-209119889
16	SP1	chr2:209119613-209120124	GM12878	blood:	n/a	chr2:209119943-209119955 chr2:209119850-209119859 chr2:209119878-209119887 chr2:209119851-209119860 chr2:209119944-209119954 chr2:209119877-209119889 chr2:209119878-209119887 chr2:209119943-209119955 chr2:209119849-209119861 chr2:209119877-209119889 chr2:209119925-209119936 chr2:209119850-209119864 chr2:209119944-209119954 chr2:209119849-209119861 chr2:209119879-209119888 chr2:209119878-209119888 chr2:209119878-209119888
17	EBF1	chr2:209119605-209120307	GM12878	blood:	n/a	chr2:209119915-209119928
18	ELF1	chr2:209119634-209120360	HepG2	liver:	n/a	n/a
19	BRCA1	chr2:209119674-209120172	GM12878	blood:	n/a	n/a
20	REST	chr2:209118863-209120379	H1-neurons	neurons:	n/a	chr2:209119866-209119879
21	RCOR1	chr2:209118644-209120330	Hela-S3	cervix:	n/a	n/a
22	ETS1	chr2:209119527-209120177	A549	lung:	n/a	chr2:209119867-209119878
23	PML	chr2:209119600-209120422	K562	blood:	n/a	n/a
24	POLR2A	chr2:209118834-209120397	HEK293	kidney:	n/a	n/a
25	POLR2A	chr2:209118485-209120368	K562	blood:	n/a	n/a
26	RCOR1	chr2:209119833-209120485	IMR90	lung:	n/a	n/a
27	TEAD4	chr2:209118072-209120414	HepG2	liver:	n/a	n/a
28	TBP	chr2:209118666-209120254	HepG2	liver:	n/a	n/a
29	HNF4A	chr2:209119879-209120321	HepG2	liver:	n/a	n/a
30	YY1	chr2:209119565-209120370	SK-N-SH_RA	brain:	n/a	chr2:209119879-209119888
31	POLR2A	chr2:209119487-209120362	PANC-1	pancreas:	n/a	n/a
32	YY1	chr2:209119488-209120497	HepG2	liver:	n/a	chr2:209119879-209119888
33	RAD21	chr2:209119771-209120463	A549	lung:	n/a	n/a
34	TAF1	chr2:209119541-209120325	HepG2	liver:	n/a	n/a
35	ELK1	chr2:209119586-209120086	GM12878	blood:	n/a	n/a
36	RAD21	chr2:209119806-209120401	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr2:209118673-209120366	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:209119512-209120287	SK-N-SH	brain:	n/a	n/a
39	NFIC	chr2:209118472-209120400	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:209118510-209120188	HepG2	liver:	n/a	n/a
41	TAF1	chr2:209119493-209120580	HepG2	liver:	n/a	n/a
42	RELA	chr2:209118515-209120334	GM15510	blood:	n/a	n/a
43	POLR2A	chr2:209118720-209120229	MCF10A-Er-Src	breast:	n/a	n/a
44	YY1	chr2:209119565-209120392	GM12892	blood:	n/a	chr2:209119879-209119888
45	POLR2A	chr2:209118835-209120365	GM18951	blood:	n/a	n/a
46	POLR2A	chr2:209118595-209120439	K562	blood:	n/a	n/a
47	MAX	chr2:209119833-209120264	K562	blood:	n/a	n/a
48	HDAC2	chr2:209119845-209120421	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:209119875-209120249	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr2:209119560-209120241	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:209119063..209119975-chr2:209130358..209131188,2	K562	blood:
2	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:
3	chr2:209095163..209099233-chr2:209117961..209120869,4	K562	blood:
4	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
5	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
6	chr2:209104117..209105753-chr2:209117843..209120211,2	MCF-7	breast:
7	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:

Variant related genes	Relation type
IDH1	TF binding region
IDH1-AS1	TF binding region
ENSG00000138413	Chromatin interaction
ENSG00000263524	Chromatin interaction
ENSG00000228380	Chromatin interaction
ENSG00000115020	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10174541	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10186350	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10194539	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198535	1.00[ASN][1000 genomes]
rs10202116	1.00[ASN][1000 genomes]
rs10497897	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10497898	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11554137	1.00[ASN][1000 genomes]
rs11685614	1.00[ASN][1000 genomes]
rs11885913	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11895188	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898653	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11901959	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12694100	0.93[EUR][1000 genomes]
rs12694101	0.97[EUR][1000 genomes]
rs13412043	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17699838	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1866046	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34218846	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3928183	1.00[ASN][1000 genomes]
rs59522113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59684347	1.00[ASN][1000 genomes]
rs6435435	1.00[ASN][1000 genomes]
rs66826643	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66887797	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67171462	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67202912	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6725418	0.94[EUR][1000 genomes]
rs67581965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67669827	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72976889	1.00[ASN][1000 genomes]
rs72989243	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056463	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73070950	1.00[ASN][1000 genomes]
rs73070958	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7557303	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7609093	0.90[AFR][1000 genomes]
rs9646838	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]

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	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209117200-209120400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:209117800-209120600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr2:209117800-209120800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:209118000-209120600	Active TSS	Ovary	ovary
5	chr2:209118000-209120600	Active TSS	Right Ventricle	heart
6	chr2:209118000-209120800	Active TSS	NHLF	lung
7	chr2:209118200-209120600	Active TSS	GM12878-XiMat	blood
8	chr2:209118200-209120800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr2:209118400-209120200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:209118400-209120200	Active TSS	Fetal Muscle Trunk	muscle
11	chr2:209118400-209120400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:209118400-209120400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:209118400-209120400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:209118400-209120400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:209118400-209120400	Active TSS	Aorta	Aorta
16	chr2:209118400-209120400	Active TSS	Brain Angular Gyrus	brain
17	chr2:209118400-209120400	Active TSS	Small Intestine	intestine
18	chr2:209118400-209120600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:209118400-209120600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:209118400-209120600	Active TSS	Left Ventricle	heart
21	chr2:209118400-209120800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:209118400-209120800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:209118600-209120200	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr2:209118600-209120200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:209118600-209120400	Active TSS	Fetal Intestine Large	intestine
26	chr2:209118600-209120400	Active TSS	Psoas Muscle	Psoas
27	chr2:209118600-209120400	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr2:209118600-209120400	Bivalent/Poised TSS	HepG2	liver
29	chr2:209118600-209120400	Active TSS	K562	blood
30	chr2:209118600-209120400	Active TSS	NHDF-Ad	bronchial
31	chr2:209118600-209120600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:209118600-209120600	Active TSS	Colonic Mucosa	Colon
33	chr2:209118600-209120600	Active TSS	Rectal Smooth Muscle	rectum
34	chr2:209118600-209120600	Active TSS	HSMMtube	muscle
35	chr2:209118600-209120800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr2:209118600-209120800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:209118600-209120800	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:209118600-209120800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr2:209118600-209120800	Active TSS	Fetal Brain Female	brain
40	chr2:209118600-209120800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr2:209118600-209120800	Active TSS	A549	lung
42	chr2:209118800-209120200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:209118800-209120200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:209118800-209120200	Active TSS	Esophagus	oesophagus
45	chr2:209118800-209120200	Active TSS	Fetal Brain Male	brain
46	chr2:209118800-209120200	Transcr. at gene 5' and 3'	Right Atrium	heart
47	chr2:209118800-209120400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:209118800-209120400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:209118800-209120400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:209118800-209120400	Active TSS	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links