Variant report

Variant	rs56824332
Chromosome Location	chr2:99771581-99771582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:516)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:516 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:99771540-99771859	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr2:99771400-99771668	GM12892	blood:	n/a	n/a
3	MYC	chr2:99771103-99771934	Hela-S3	cervix:	n/a	chr2:99771561-99771570
4	GABPA	chr2:99771221-99771821	HepG2	liver:	n/a	chr2:99771586-99771595 chr2:99771522-99771529
5	FOSL2	chr2:99771082-99771902	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:99771097-99771891	HepG2	liver:	n/a	n/a
7	BCL11A	chr2:99771362-99771684	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:99770986-99772188	K562	blood:	n/a	n/a
9	BACH1	chr2:99771099-99771837	H1-hESC	embryonic stem cell:	n/a	n/a
10	WRNIP1	chr2:99770718-99772356	GM12878	blood:	n/a	n/a
11	TBP	chr2:99771040-99772001	K562	blood:	n/a	n/a
12	MAX	chr2:99771116-99772026	NB4	blood:	n/a	chr2:99771561-99771570
13	POLR2A	chr2:99770521-99772535	GM12892	blood:	n/a	n/a
14	CREB1	chr2:99771260-99771730	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr2:99770692-99772100	GM12892	blood:	n/a	n/a
16	FOXP2	chr2:99771229-99771819	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr2:99770891-99772472	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:99770271-99772617	K562	blood:	n/a	n/a
19	HDAC2	chr2:99771043-99771941	MCF-7	breast:	n/a	chr2:99771561-99771570
20	GABPA	chr2:99771240-99771815	HepG2	liver:	n/a	chr2:99771586-99771595 chr2:99771522-99771529
21	POLR2A	chr2:99771061-99771853	HUVEC	blood vessel:	n/a	n/a
22	RELA	chr2:99771036-99771995	GM10847	blood:	n/a	n/a
23	POLR2A	chr2:99770983-99772014	GM12878	blood:	n/a	n/a
24	SP1	chr2:99770980-99771954	A549	lung:	n/a	n/a
25	MYC	chr2:99771369-99771809	MCF-7	breast:	n/a	chr2:99771561-99771570
26	POLR2A	chr2:99770800-99771994	U87	brain:	n/a	n/a
27	FOXA2	chr2:99771346-99772022	A549	lung:	n/a	n/a
28	POLR2A	chr2:99770913-99772008	K562	blood:	n/a	n/a
29	POLR2A	chr2:99770958-99772008	ECC-1	luminal epithelium:	n/a	n/a
30	USF2	chr2:99771074-99771620	H1-hESC	embryonic stem cell:	n/a	n/a
31	MXI1	chr2:99770917-99772125	GM12878	blood:	n/a	n/a
32	E2F4	chr2:99771043-99771728	GM12878	blood:	n/a	n/a
33	NFIC	chr2:99770745-99772019	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:99770989-99772526	K562	blood:	n/a	n/a
35	POLR2A	chr2:99770535-99772543	HepG2	liver:	n/a	n/a
36	PAX5	chr2:99771227-99771661	GM12892	blood:	n/a	n/a
37	TAF1	chr2:99771187-99771823	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:99771041-99772010	K562	blood:	n/a	n/a
39	POLR2A	chr2:99771132-99771736	A549	lung:	n/a	n/a
40	EGR1	chr2:99771253-99771860	K562	blood:	n/a	chr2:99771559-99771572 chr2:99771561-99771571 chr2:99771559-99771573 chr2:99771560-99771571 chr2:99771562-99771571 chr2:99771559-99771572 chr2:99771555-99771577 chr2:99771560-99771574 chr2:99771561-99771571 chr2:99771559-99771572
41	ZKSCAN1	chr2:99770679-99771850	Hela-S3	cervix:	n/a	n/a
42	ATF2	chr2:99771101-99771849	GM12878	blood:	n/a	n/a
43	ELK1	chr2:99771286-99771907	GM12878	blood:	n/a	n/a
44	NFATC1	chr2:99770958-99771924	GM12878	blood:	n/a	n/a
45	REST	chr2:99770775-99772194	H1-neurons	neurons:	n/a	chr2:99771669-99771683
46	E2F6	chr2:99771103-99771721	K562	blood:	n/a	n/a
47	HEY1	chr2:99771030-99771901	K562	blood:	n/a	n/a
48	MYC	chr2:99770962-99772118	K562	blood:	n/a	chr2:99771561-99771570
49	JUND	chr2:99771241-99771897	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:99771032-99772023	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:99771531-99771581	Jurkat	blood:	n/a
2	chr2:99771531-99771581	H1-hESC	embryonic stem cell:	embryo
3	chr2:99771531-99771581	BE2_C	brain:	n/a
4	chr2:99771531-99771581	PFSK-1	brain:	n/a
5	chr2:99771531-99771581	IMR90	lung:	fetal
6	chr2:99771531-99771581	HCM	heart:	n/a
7	chr2:99771531-99771581	ovcar-3	ovarian:	n/a
8	chr2:99771531-99771581	T-47D	breast:	n/a
9	chr2:99771531-99771581	HMEC	breast:	n/a
10	chr2:99771531-99771581	GM06990	blood:	n/a
11	chr2:99771531-99771581	HCPEpiC	choroid plexus:	n/a
12	chr2:99771531-99771581	PrEC	prostate:	n/a
13	chr2:99771531-99771581	HPAEpiC	pulmonary alveolar:	n/a
14	chr2:99771531-99771581	HCF	heart:	n/a
15	chr2:99771531-99771581	Hela-S3	cervix:	n/a
16	chr2:99771531-99771581	HL-60	blood:	n/a
17	chr2:99771531-99771581	NH-A	brain:	n/a
18	chr2:99771531-99771581	NT2-D1	testis:	n/a
19	chr2:99771531-99771581	HRCEpiC	kidney:	n/a
20	chr2:99771531-99771581	BJ	skin:	n/a
21	chr2:99771531-99771581	PANC-1	pancreas:	n/a
22	chr2:99771531-99771581	K562	blood:	n/a
23	chr2:99771531-99771581	GM12891	blood:	n/a
24	chr2:99771531-99771581	HNPCEpiC	eye:	n/a
25	chr2:99771531-99771581	HepG2	liver:	n/a
26	chr2:99771531-99771581	SKMC	muscle:	n/a
27	chr2:99771531-99771581	MCF-7	breast:	n/a
28	chr2:99771531-99771581	NHDF-neo	bronchial:	n/a
29	chr2:99771531-99771581	SK-N-SH	brain:	n/a
30	chr2:99771531-99771581	CMK	blood:	n/a
31	chr2:99771531-99771581	HAEpiC	amniotic membrane:	n/a
32	chr2:99771531-99771581	AG04449	skin:	fetal
33	chr2:99771531-99771581	AG09319	gingival:	n/a
34	chr2:99771531-99771581	NB4	blood:	n/a
35	chr2:99771531-99771581	AG09309	skin:	n/a
36	chr2:99771531-99771581	AG04450	lung:	fetal
37	chr2:99771531-99771581	ProgFib	skin:	n/a
38	chr2:99771531-99771581	HEK293	kidney:	embryo
39	chr2:99771531-99771581	ECC-1	luminal epithelium:	n/a
40	chr2:99771531-99771581	AG10803	skin:	n/a
41	chr2:99771531-99771581	HRE	kidney:	n/a
42	chr2:99771531-99771581	Caco-2	colon:	n/a
43	chr2:99771531-99771581	GM12878	blood:	n/a
44	chr2:99771531-99771581	HCT-116	colon:	n/a
45	chr2:99771531-99771581	RPTEC	kidney:	n/a
46	chr2:99771531-99771581	Hepatocyte	liver:	n/a
47	chr2:99771531-99771581	SK-N-MC	brain:	n/a
48	chr2:99771531-99771581	NHBE	bronchial:	n/a
49	chr2:99771531-99771581	AoSMC	blood vessel:	n/a
50	chr2:99771531-99771581	HUVEC	blood vessel:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99754528..99760418-chr2:99769364..99773305,11	K562	blood:
2	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
3	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
4	chr2:99769803..99772533-chr2:99952128..99954259,2	MCF-7	breast:
5	chr2:99756639..99759461-chr2:99768691..99772730,10	MCF-7	breast:
6	chr2:99769128..99773388-chr2:99951603..99955259,4	K562	blood:
7	chr2:99768084..99772423-chr2:99795960..99799744,7	K562	blood:
8	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
9	chr2:99771362..99771866-chr3:101568039..101568603,2	HCT-116	colon:
10	chr2:99770250..99773199-chr2:99783967..99787710,4	MCF-7	breast:
11	chr2:99770887..99773276-chr2:99955255..99957900,2	MCF-7	breast:
12	chr1:109234367..109235217-chr2:99770725..99771724,3	Hela-S3	cervix:
13	chr16:56965668..56966219-chr2:99771568..99772101,2	Hela-S3	cervix:
14	chr12:46766088..46766800-chr2:99771421..99772015,2	NB4	blood:
15	chr2:99769755..99772454-chr2:99953389..99955420,3	K562	blood:
16	chr2:99755030..99760884-chr2:99769021..99772906,10	K562	blood:

No data

Variant related genes	Relation type
TSGA10	TF binding region
TSGA10	CpG island
ENSG00000135951	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000134186	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000144802	Chromatin interaction
ENSG00000273045	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000241962	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs56379415	1.00[EUR][1000 genomes]
rs6710670	1.00[AMR][1000 genomes]
rs7579984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7607487	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr2:99770200-99772600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:99770400-99772200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99770400-99772200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:99770400-99772200	Active TSS	Right Ventricle	heart
5	chr2:99770400-99772400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:99770400-99772400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:99770400-99772400	Active TSS	Left Ventricle	heart
8	chr2:99770400-99772600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:99770400-99772600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:99770400-99772600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:99770400-99772600	Active TSS	NHLF	lung
12	chr2:99770600-99772000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr2:99770600-99772000	Active TSS	Fetal Brain Male	brain
14	chr2:99770600-99772200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:99770600-99772200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:99770600-99772200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:99770600-99772200	Active TSS	Colonic Mucosa	Colon
18	chr2:99770600-99772200	Active TSS	Psoas Muscle	Psoas
19	chr2:99770600-99772400	Active TSS	NHDF-Ad	bronchial
20	chr2:99770600-99772600	Active TSS	Fetal Muscle Trunk	muscle
21	chr2:99770600-99772600	Active TSS	HSMMtube	muscle
22	chr2:99770800-99772000	Active TSS	Colon Smooth Muscle	Colon
23	chr2:99770800-99772000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:99770800-99772200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:99770800-99772200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:99770800-99772200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr2:99770800-99772200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:99770800-99772200	Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:99770800-99772200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:99770800-99772200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:99770800-99772200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:99770800-99772200	Active TSS	Aorta	Aorta
33	chr2:99770800-99772400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:99770800-99772400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:99770800-99772400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:99770800-99772400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:99770800-99772400	Active TSS	Pancreas	Pancrea
38	chr2:99770800-99772600	Active TSS	Fetal Intestine Large	intestine
39	chr2:99770800-99772600	Active TSS	Ovary	ovary
40	chr2:99770800-99772600	Active TSS	Right Atrium	heart
41	chr2:99770800-99772800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:99770800-99772800	Active TSS	Brain Hippocampus Middle	brain
43	chr2:99770800-99772800	Active TSS	A549	lung
44	chr2:99771000-99771800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:99771000-99771800	Active TSS	Fetal Brain Female	brain
46	chr2:99771000-99771800	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:99771000-99772000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:99771000-99772000	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr2:99771000-99772000	Active TSS	Brain Angular Gyrus	brain
50	chr2:99771000-99772000	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links