Variant report

Variant	rs72940556
Chromosome Location	chr2:85764506-85764507
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:31)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr2:85764471-85768062	A549	lung:	n/a	n/a
2	POLR2A	chr2:85764187-85776473	PBDE	blood:	n/a	n/a
3	POLR2A	chr2:85764404-85775965	GM12878	blood:	n/a	n/a
4	HEY1	chr2:85764198-85764590	K562	blood:	n/a	n/a
5	IRF1	chr2:85764312-85767853	K562	blood:	n/a	chr2:85765285-85765299 chr2:85764705-85764717 chr2:85767337-85767346 chr2:85767338-85767352
6	POLR2A	chr2:85764340-85770626	GM12891	blood:	n/a	n/a
7	BCL3	chr2:85764487-85768038	A549	lung:	n/a	chr2:85767948-85767957 chr2:85766915-85766928 chr2:85766117-85766130 chr2:85765161-85765170 chr2:85765969-85765982 chr2:85767338-85767347
8	REST	chr2:85763518-85767607	H1-neurons	neurons:	n/a	chr2:85766116-85766129 chr2:85766157-85766170 chr2:85766157-85766170 chr2:85766274-85766287 chr2:85765620-85765628 chr2:85764843-85764856
9	SREBP1	chr2:85763798-85768460	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:85764195-85777893	PANC-1	pancreas:	n/a	n/a
11	CTCF	chr2:85763722-85768035	A549	lung:	n/a	n/a
12	TEAD4	chr2:85764498-85767624	K562	blood:	n/a	n/a
13	POLR2A	chr2:85764425-85776507	U87	brain:	n/a	n/a
14	POLR2A	chr2:85764254-85778359	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr2:85764329-85770781	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr2:85763373-85768685	SK-N-SH	brain:	n/a	chr2:85766928-85766937
17	POLR2A	chr2:85763721-85768325	MCF10A-Er-Src	breast:	n/a	n/a
18	MXI1	chr2:85764453-85765384	K562	blood:	n/a	n/a
19	EP300	chr2:85764505-85767547	K562	blood:	n/a	chr2:85766558-85766574
20	POLR2A	chr2:85764419-85776508	U87	brain:	n/a	n/a
21	MTA3	chr2:85764231-85767813	GM12878	blood:	n/a	n/a
22	FOSL2	chr2:85764274-85767942	A549	lung:	n/a	chr2:85765583-85765592 chr2:85765508-85765522 chr2:85766871-85766880 chr2:85765968-85765977
23	POLR2A	chr2:85764279-85775944	HepG2	liver:	n/a	n/a
24	MYC	chr2:85764336-85764849	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr2:85763991-85776489	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:85764307-85775325	K562	blood:	n/a	n/a
27	POLR2A	chr2:85764221-85764525	HepG2	liver:	n/a	n/a
28	JUND	chr2:85763443-85767859	SK-N-SH	brain:	n/a	chr2:85765583-85765592 chr2:85765508-85765522 chr2:85766871-85766880 chr2:85765968-85765977
29	POLR2A	chr2:85764289-85776546	K562	blood:	n/a	n/a
30	HCFC1	chr2:85764392-85768179	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr2:85764083-85776617	PANC-1	pancreas:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:85764479-85764529	SK-N-SH_RA	brain:	n/a
2	chr2:85764479-85764529	HNPCEpiC	eye:	n/a
3	chr2:85764479-85764529	AG09309	skin:	n/a
4	chr2:85764479-85764529	LNCaP	prostate:	n/a
5	chr2:85764479-85764529	HRCEpiC	kidney:	n/a
6	chr2:85764479-85764529	RPTEC	kidney:	n/a
7	chr2:85764479-85764529	GM12892	blood:	n/a
8	chr2:85764479-85764529	ECC-1	luminal epithelium:	n/a
9	chr2:85764479-85764529	HUVEC	blood vessel:	n/a
10	chr2:85764479-85764529	GM12878	blood:	n/a
11	chr2:85764479-85764529	CMK	blood:	n/a
12	chr2:85764479-85764529	MCF-7	breast:	n/a
13	chr2:85764479-85764529	HepG2	liver:	n/a
14	chr2:85764479-85764529	HMEC	breast:	n/a
15	chr2:85764479-85764529	NH-A	brain:	n/a
16	chr2:85764479-85764529	Hepatocyte	liver:	n/a
17	chr2:85764479-85764529	SKMC	muscle:	n/a
18	chr2:85764479-85764529	PANC-1	pancreas:	n/a
19	chr2:85764479-85764529	SAEC	small airway:	n/a
20	chr2:85764479-85764529	GM12891	blood:	n/a
21	chr2:85764479-85764529	IMR90	lung:	fetal
22	chr2:85764479-85764529	BJ	skin:	n/a
23	chr2:85764479-85764529	SK-N-MC	brain:	n/a
24	chr2:85764479-85764529	Caco-2	colon:	n/a
25	chr2:85764479-85764529	HEEpiC	esophagus:	n/a
26	chr2:85764479-85764529	GM06990	blood:	n/a
27	chr2:85764479-85764529	MCF10A-Er-Src	breast:	n/a
28	chr2:85764479-85764529	HAEpiC	amniotic membrane:	n/a
29	chr2:85764479-85764529	AG04449	skin:	fetal
30	chr2:85764479-85764529	NHBE	bronchial:	n/a
31	chr2:85764479-85764529	NB4	blood:	n/a
32	chr2:85764479-85764529	AG10803	skin:	n/a
33	chr2:85764479-85764529	PrEC	prostate:	n/a
34	chr2:85764479-85764529	NHDF-neo	bronchial:	n/a
35	chr2:85764479-85764529	SK-N-SH	brain:	n/a
36	chr2:85764479-85764529	HEK293	kidney:	embryo
37	chr2:85764479-85764529	HCF	heart:	n/a
38	chr2:85764479-85764529	HL-60	blood:	n/a
39	chr2:85764479-85764529	T-47D	breast:	n/a
40	chr2:85764479-85764529	AG09319	gingival:	n/a
41	chr2:85764479-85764529	HRE	kidney:	n/a
42	chr2:85764479-85764529	BE2_C	brain:	n/a
43	chr2:85764479-85764529	Jurkat	blood:	n/a
44	chr2:85764479-85764529	GM19239	blood:	n/a
45	chr2:85764479-85764529	Hela-S3	cervix:	n/a
46	chr2:85764479-85764529	ProgFib	skin:	n/a
47	chr2:85764479-85764529	U87	brain:	n/a
48	chr2:85764479-85764529	ovcar-3	ovarian:	n/a
49	chr2:85764479-85764529	NT2-D1	testis:	n/a
50	chr2:85764479-85764529	PFSK-1	brain:	n/a

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85551217..85557082-chr2:85763566..85768403,18	K562	blood:
2	chr2:85579454..85586122-chr2:85763967..85769855,18	K562	blood:
3	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
4	chr2:85699337..85700838-chr2:85763015..85764537,2	K562	blood:
5	chr2:85763361..85766337-chr6:3257277..3259286,2	MCF-7	breast:
6	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
7	chr2:85764353..85768297-chr2:85801597..85805697,4	K562	blood:
8	chr2:85549396..85557177-chr2:85763484..85769653,16	MCF-7	breast:
9	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
10	chr2:85593223..85597895-chr2:85762999..85767407,5	K562	blood:
11	chr2:85676312..85679045-chr2:85763081..85764997,2	MCF-7	breast:
12	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
13	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
14	chr2:85764186..85766717-chr9:131486656..131488978,2	MCF-7	breast:
15	chr2:85525647..85527458-chr2:85764412..85766589,2	K562	blood:
16	chr2:85684691..85688557-chr2:85764007..85767922,5	MCF-7	breast:
17	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
18	chr2:85764278..85767937-chr2:85842194..85845131,5	K562	blood:
19	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
20	chr2:85764408..85765579-chr3:149089258..149090120,3	Hela-S3	cervix:
21	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
22	chr2:85627012..85628603-chr2:85761794..85764774,2	MCF-7	breast:
23	chr2:85764346..85769986-chr2:85836202..85840842,10	MCF-7	breast:
24	chr2:85658029..85667242-chr2:85763719..85770665,19	MCF-7	breast:
25	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
26	chr2:85551607..85557241-chr2:85763492..85768403,12	K562	blood:
27	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
28	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:
29	chr19:2474969..2476737-chr2:85764259..85767220,2	MCF-7	breast:
30	chr2:85763670..85765821-chr8:103626482..103628090,2	MCF-7	breast:
31	chr2:85764476..85768967-chr2:85811222..85814196,4	MCF-7	breast:

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

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

No data

Variant related genes	Relation type
MAT2A	TF binding region
RN7SL830P	TF binding region
RN7SL830P	CpG island
MAT2A	CpG island
ENSG00000242095	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000099860	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000221579	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000223478	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000202382	Chromatin interaction
ENSG00000180822	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000152291	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs57313428	0.96[AFR][1000 genomes]
rs58540395	0.94[AFR][1000 genomes]
rs59229326	0.96[AFR][1000 genomes]
rs6723678	0.94[AFR][1000 genomes]
rs6751560	0.94[AFR][1000 genomes]
rs72923003	0.94[AFR][1000 genomes]
rs72940558	0.96[AFR][1000 genomes]
rs72940569	0.94[AFR][1000 genomes]
rs72940575	0.96[AFR][1000 genomes]
rs7592171	0.92[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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
2	chr2:85752000-85764800	Weak transcription	Gastric	stomach
3	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:85761400-85764600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:85761400-85764600	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:85761600-85764600	Enhancers	Fetal Intestine Small	intestine
8	chr2:85763400-85764800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:85763600-85764600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:85763600-85764600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:85763600-85764600	Enhancers	Fetal Intestine Large	intestine
12	chr2:85763600-85764800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:85763600-85765000	Enhancers	Fetal Heart	heart
14	chr2:85763600-85765000	Flanking Active TSS	HSMM	muscle
15	chr2:85763600-85765200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr2:85763600-85767000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:85763800-85764600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:85763800-85764600	Enhancers	Fetal Lung	lung
19	chr2:85763800-85764800	Enhancers	Left Ventricle	heart
20	chr2:85763800-85765800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:85764000-85764600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:85764000-85764600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:85764000-85764600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:85764000-85764600	Enhancers	Primary T cells from cord blood	blood
25	chr2:85764000-85764600	Enhancers	Fetal Muscle Leg	muscle
26	chr2:85764000-85764600	Enhancers	Fetal Thymus	thymus
27	chr2:85764000-85764600	Flanking Active TSS	HSMMtube	muscle
28	chr2:85764000-85764800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr2:85764000-85764800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:85764000-85764800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:85764000-85764800	Weak transcription	Pancreas	Pancrea
32	chr2:85764000-85765200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr2:85764000-85765600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:85764000-85765800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:85764000-85767600	Active TSS	Psoas Muscle	Psoas
36	chr2:85764200-85764600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:85764200-85764600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:85764200-85764600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:85764200-85764600	Enhancers	Primary B cells from cord blood	blood
40	chr2:85764200-85764600	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr2:85764200-85764600	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr2:85764200-85764600	Flanking Active TSS	Fetal Kidney	kidney
43	chr2:85764200-85764600	Enhancers	Fetal Stomach	stomach
44	chr2:85764200-85764600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr2:85764200-85764600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:85764200-85764600	Flanking Active TSS	GM12878-XiMat	blood
47	chr2:85764200-85764600	Flanking Active TSS	HepG2	liver
48	chr2:85764200-85764800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:85764200-85764800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:85764200-85764800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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