Variant report

Variant	rs72940558
Chromosome Location	chr2:85765471-85765472
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	SMARCB1	chr2:85764694-85767671	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:85764762-85767800	GM19099	blood:	n/a	n/a
3	POLR2A	chr2:85764818-85775931	U87	brain:	n/a	n/a
4	POLR2A	chr2:85764716-85770554	GM12878	blood:	n/a	n/a
5	SIX5	chr2:85764471-85768062	A549	lung:	n/a	n/a
6	MAX	chr2:85764848-85767481	K562	blood:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
7	TAF1	chr2:85765448-85766986	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:85764187-85776473	PBDE	blood:	n/a	n/a
9	ETS1	chr2:85765327-85767597	A549	lung:	n/a	chr2:85766269-85766282 chr2:85766275-85766286
10	TEAD4	chr2:85765460-85766693	A549	lung:	n/a	n/a
11	TAF1	chr2:85764787-85766947	K562	blood:	n/a	n/a
12	POLR2A	chr2:85764724-85767620	GM12878	blood:	n/a	n/a
13	ELF1	chr2:85765381-85767190	GM12878	blood:	n/a	chr2:85766833-85766845 chr2:85765886-85765898 chr2:85766564-85766576
14	RELA	chr2:85764766-85767240	GM15510	blood:	n/a	n/a
15	POLR2A	chr2:85764748-85775047	K562	blood:	n/a	n/a
16	MAX	chr2:85765280-85767502	ECC-1	luminal epithelium:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
17	MYC	chr2:85764769-85767714	K562	blood:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
18	CHD1	chr2:85764772-85767796	GM12878	blood:	n/a	chr2:85766159-85766169
19	PML	chr2:85765237-85767040	K562	blood:	n/a	n/a
20	MAX	chr2:85764529-85767926	A549	lung:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
21	SIN3AK20	chr2:85764700-85767781	MCF-7	breast:	n/a	n/a
22	BACH1	chr2:85764731-85767050	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr2:85764700-85767728	GM12891	blood:	n/a	n/a
24	YY1	chr2:85765470-85766022	GM12892	blood:	n/a	chr2:85765766-85765788 chr2:85765853-85765864 chr2:85765644-85765652 chr2:85765642-85765654 chr2:85765643-85765665 chr2:85765777-85765785 chr2:85765643-85765653 chr2:85765772-85765789
25	POLR2A	chr2:85765419-85767105	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:85764667-85767840	HepG2	liver:	n/a	n/a
27	MYC	chr2:85764889-85767689	MCF10A-Er-Src	breast:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
28	POLR2A	chr2:85764704-85767819	GM18505	blood:	n/a	n/a
29	POLR2A	chr2:85765282-85767893	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr2:85764404-85775965	GM12878	blood:	n/a	n/a
31	MYC	chr2:85764747-85767611	NB4	blood:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
32	POLR2A	chr2:85764751-85767227	GM15510	blood:	n/a	n/a
33	POLR2A	chr2:85764647-85767716	K562	blood:	n/a	n/a
34	POLR2A	chr2:85764734-85766654	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:85764649-85768074	GM12892	blood:	n/a	n/a
36	EP300	chr2:85765365-85767449	A549	lung:	n/a	chr2:85766558-85766574
37	POLR2A	chr2:85764666-85767973	HUVEC	blood vessel:	n/a	n/a
38	YY1	chr2:85764673-85767217	HepG2	liver:	n/a	chr2:85765766-85765788 chr2:85766125-85766136 chr2:85765853-85765864 chr2:85765644-85765652 chr2:85765642-85765654 chr2:85766127-85766141 chr2:85765643-85765665 chr2:85765777-85765785 chr2:85765162-85765171 chr2:85765643-85765653 chr2:85765772-85765789 chr2:85766273-85766287
39	POLR2A	chr2:85764728-85767223	GM18951	blood:	n/a	n/a
40	POLR2A	chr2:85764668-85765471	HepG2	liver:	n/a	n/a
41	MYBL2	chr2:85764639-85768149	HepG2	liver:	n/a	n/a
42	ZBTB7A	chr2:85764778-85766421	K562	blood:	n/a	n/a
43	IRF1	chr2:85764312-85767853	K562	blood:	n/a	chr2:85765285-85765299 chr2:85764705-85764717 chr2:85767337-85767346 chr2:85767338-85767352
44	POLR2A	chr2:85764617-85775797	GM12892	blood:	n/a	n/a
45	MAX	chr2:85765383-85767800	HCT-116	colon:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
46	POLR2A	chr2:85764340-85770626	GM12891	blood:	n/a	n/a
47	POLR2A	chr2:85764661-85767972	K562	blood:	n/a	n/a
48	POLR2A	chr2:85764715-85767899	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr2:85764710-85767951	MCF-7	breast:	n/a	n/a
50	TAF1	chr2:85765398-85766965	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85594968..85598599-chr2:85764725..85768388,5	K562	blood:
2	chr2:85647793..85648787-chr2:85765071..85765577,2	Hela-S3	cervix:
3	chr15:83875619..83876249-chr2:85765428..85766252,2	Hela-S3	cervix:
4	chr2:85551217..85557082-chr2:85763566..85768403,18	K562	blood:
5	chr2:85579454..85586122-chr2:85763967..85769855,18	K562	blood:
6	chr2:85765063..85766032-chr3:88108256..88108913,2	Hela-S3	cervix:
7	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
8	chr2:85765143..85767907-chr2:85841259..85844982,5	MCF-7	breast:
9	chr2:85764946..85769175-chr2:85814893..85818821,4	K562	blood:
10	chr2:85647528..85648758-chr2:85765454..85766138,3	MCF-7	breast:
11	chr17:73150326..73150964-chr2:85764756..85765624,2	Hela-S3	cervix:
12	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
13	chr2:85554021..85557000-chr2:85764755..85766329,2	MCF-7	breast:
14	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
15	chr2:85765276..85767700-chr2:85863355..85867135,3	MCF-7	breast:
16	chr2:85763361..85766337-chr6:3257277..3259286,2	MCF-7	breast:
17	chr2:85764842..85767974-chr2:85803132..85805827,5	MCF-7	breast:
18	chr2:85764843..85765538-chr6:35419907..35420537,2	Hela-S3	cervix:
19	chr2:85571438..85573879-chr2:85765048..85766873,2	K562	blood:
20	chr17:77782933..77785635-chr2:85764990..85767788,2	K562	blood:
21	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:
22	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
23	chr2:85639277..85641952-chr2:85764715..85768056,5	MCF-7	breast:
24	chr2:85764353..85768297-chr2:85801597..85805697,4	K562	blood:
25	chr2:85549396..85557177-chr2:85763484..85769653,16	MCF-7	breast:
26	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
27	chr2:85593223..85597895-chr2:85762999..85767407,5	K562	blood:
28	chr2:85764979..85767733-chr6:26155953..26157777,2	MCF-7	breast:
29	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
30	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
31	chr2:85764186..85766717-chr9:131486656..131488978,2	MCF-7	breast:
32	chr2:85525647..85527458-chr2:85764412..85766589,2	K562	blood:
33	chr17:60780153..60782925-chr2:85765178..85767837,2	MCF-7	breast:
34	chr2:85627997..85630294-chr2:85764975..85768258,3	K562	blood:
35	chr2:85684691..85688557-chr2:85764007..85767922,5	MCF-7	breast:
36	chr2:85765298..85767706-chr2:85816811..85818953,3	MCF-7	breast:
37	chr2:85765001..85768151-chr2:85794146..85798905,4	K562	blood:
38	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
39	chr2:85668932..85671543-chr2:85764847..85767171,3	MCF-7	breast:
40	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
41	chr2:85765167..85768270-chr2:85828920..85831672,3	K562	blood:
42	chr2:85764278..85767937-chr2:85842194..85845131,5	K562	blood:
43	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
44	chr13:91999993..92001632-chr2:85765128..85766944,2	K562	blood:
45	chr2:85764966..85765592-chr2:201980876..201981423,2	Hela-S3	cervix:
46	chr14:23235603..23236302-chr2:85765317..85766156,2	Hela-S3	cervix:
47	chr2:85764408..85765579-chr3:149089258..149090120,3	Hela-S3	cervix:
48	chr2:85572304..85574564-chr2:85765352..85768269,2	MCF-7	breast:
49	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
50	chr10:122610881..122611432-chr2:85765284..85765790,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCX-3	chr2:85763939-85766100	NONHSAT072013
2	lnc-GGCX-3	chr2:85764590-85766009	NONHSAT072014

Variant related genes	Relation type
MAT2A	TF binding region
ENSG00000099860	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000176407	Chromatin interaction
ENSG00000187118	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000258458	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000266536	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000145041	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000120008	Chromatin interaction
ENSG00000221579	Chromatin interaction
ENSG00000152284	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000229729	Chromatin interaction
ENSG00000173838	Chromatin interaction
ENSG00000180822	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000202382	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000242095	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000003402	Chromatin interaction
ENSG00000223478	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000155463	Chromatin interaction
ENSG00000238331	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12470957	1.00[ASN][1000 genomes]
rs17026452	1.00[ASN][1000 genomes]
rs57313428	0.92[AFR][1000 genomes]
rs57922790	1.00[ASN][1000 genomes]
rs58540395	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59229326	0.92[AFR][1000 genomes]
rs6723678	0.98[AFR][1000 genomes]
rs6751560	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72923003	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72938596	1.00[ASN][1000 genomes]
rs72940556	0.96[AFR][1000 genomes]
rs72940569	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72940575	0.92[AFR][1000 genomes]
rs7592171	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 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	chr2:85763600-85767000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:85763800-85765800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:85764000-85765600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:85764000-85765800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:85764000-85767600	Active TSS	Psoas Muscle	Psoas
6	chr2:85764200-85765600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:85764200-85765600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr2:85764200-85765600	Flanking Active TSS	Fetal Brain Male	brain
9	chr2:85764200-85765600	Flanking Active TSS	Osteobl	bone
10	chr2:85764200-85766200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:85764200-85768600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:85764400-85765600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:85764400-85765800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:85764400-85765800	Flanking Active TSS	HUVEC	blood vessel
15	chr2:85764400-85767000	Active TSS	K562	blood
16	chr2:85764400-85767600	Active TSS	NHDF-Ad	bronchial
17	chr2:85764600-85765600	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr2:85764600-85766000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr2:85764600-85766800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:85764600-85767000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr2:85764600-85767000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:85764600-85767000	Active TSS	Brain Anterior Caudate	brain
23	chr2:85764600-85767200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:85764600-85767200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:85764600-85768200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:85764600-85768200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr2:85764600-85768200	Active TSS	Brain Angular Gyrus	brain
28	chr2:85764600-85768200	Active TSS	Fetal Stomach	stomach
29	chr2:85764600-85768600	Active TSS	Aorta	Aorta
30	chr2:85764800-85765600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr2:85764800-85765600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:85764800-85765600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:85764800-85765800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:85764800-85765800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr2:85764800-85766200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:85764800-85766800	Active TSS	A549	lung
37	chr2:85764800-85767000	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:85764800-85767000	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr2:85764800-85767200	Transcr. at gene 5' and 3'	Right Atrium	heart
40	chr2:85764800-85767400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:85764800-85767400	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:85764800-85767400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr2:85764800-85767600	Active TSS	Spleen	Spleen
44	chr2:85764800-85767800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr2:85764800-85768000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:85764800-85768000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:85764800-85768000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr2:85764800-85768200	Active TSS	Lung	lung
49	chr2:85764800-85768400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:85764800-85768400	Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links