Variant report

Variant	rs11682732
Chromosome Location	chr2:62733668-62733669
allele	C/T
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	EP300	chr2:62732672-62733793	A549	lung:	n/a	chr2:62732763-62732772
2	POLR2A	chr2:62732438-62733722	K562	blood:	n/a	n/a
3	SIN3AK20	chr2:62733425-62733900	A549	lung:	n/a	n/a
4	USF1	chr2:62733375-62734011	A549	lung:	n/a	n/a
5	EP300	chr2:62732876-62733734	K562	blood:	n/a	n/a
6	BHLHE40	chr2:62732400-62733822	K562	blood:	n/a	chr2:62732965-62732981
7	POLR2A	chr2:62732681-62733795	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:62732724-62733744	K562	blood:	n/a	n/a
9	MXI1	chr2:62733412-62733895	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:62732848-62733775	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr2:62733090-62733681	Hela-S3	cervix:	n/a	n/a
12	HDAC2	chr2:62732859-62733695	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:62732452-62733730	K562	blood:	n/a	n/a
14	EP300	chr2:62733551-62733906	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:62732742-62733783	GM19099	blood:	n/a	n/a
16	TAF1	chr2:62732703-62733931	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr2:62732297-62733668	H1-hESC	embryonic stem cell:	n/a	chr2:62732906-62732915
18	POLR2A	chr2:62732598-62733711	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr2:62732236-62733695	K562	blood:	n/a	chr2:62732974-62732986 chr2:62732763-62732773 chr2:62732975-62732986
20	PML	chr2:62732677-62733843	GM12878	blood:	n/a	n/a
21	FOSL2	chr2:62732643-62733803	A549	lung:	n/a	chr2:62732753-62732767
22	POLR2A	chr2:62732777-62733746	HCT-116	colon:	n/a	n/a
23	POLR2A	chr2:62732823-62733721	HCT-116	colon:	n/a	n/a
24	KAP1	chr2:62732897-62733847	U2OS	brain:	n/a	n/a
25	POLR2A	chr2:62733060-62733686	Hela-S3	cervix:	n/a	n/a
26	USF1	chr2:62733362-62733954	ECC-1	luminal epithelium:	n/a	n/a
27	JUND	chr2:62732340-62733743	K562	blood:	n/a	chr2:62732753-62732767
28	TBP	chr2:62732351-62733745	K562	blood:	n/a	n/a
29	YY1	chr2:62732660-62733689	SK-N-SH	brain:	n/a	chr2:62732757-62732771 chr2:62733069-62733091 chr2:62733069-62733079
30	BCL3	chr2:62732715-62733916	A549	lung:	n/a	n/a
31	MAX	chr2:62732674-62733761	MCF-7	breast:	n/a	chr2:62732906-62732915 chr2:62733706-62733715
32	GTF2F1	chr2:62733484-62733764	H1-hESC	embryonic stem cell:	n/a	n/a
33	TEAD4	chr2:62732780-62733771	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr2:62732433-62733834	ProgFib	skin:	n/a	n/a
35	MAZ	chr2:62732652-62733923	IMR90	lung:	n/a	chr2:62732906-62732915 chr2:62733706-62733715
36	HEY1	chr2:62732723-62733685	K562	blood:	n/a	chr2:62732758-62732773
37	POLR2A	chr2:62732743-62734017	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr2:62732862-62733838	SK-N-MC	brain:	n/a	n/a
39	GATA1	chr2:62732342-62733859	PBDE	blood:	n/a	n/a
40	MAX	chr2:62733005-62733746	Hela-S3	cervix:	n/a	chr2:62733706-62733715
41	CREB1	chr2:62732659-62733766	K562	blood:	n/a	n/a
42	MYC	chr2:62732754-62733688	K562	blood:	n/a	chr2:62732906-62732915
43	USF1	chr2:62733281-62733918	SK-N-SH	brain:	n/a	n/a
44	USF1	chr2:62732853-62733909	ECC-1	luminal epithelium:	n/a	chr2:62732965-62732981
45	USF1	chr2:62733482-62733823	H1-hESC	embryonic stem cell:	n/a	n/a
46	SMC3	chr2:62733134-62733803	Hela-S3	cervix:	n/a	n/a
47	GTF2F1	chr2:62732936-62733686	K562	blood:	n/a	n/a
48	TAF1	chr2:62732663-62733692	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr2:62732652-62733795	U87	brain:	n/a	n/a
50	POLR2A	chr2:62732732-62733717	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:62732196..62734647-chr2:62932204..62934327,2	K562	blood:
2	chr2:62733287..62736036-chr2:62952497..62954456,3	MCF-7	breast:
3	chr2:62732443..62734653-chr2:62900758..62903078,2	MCF-7	breast:
4	chr2:62730719..62734296-chr2:62930912..62935708,9	MCF-7	breast:
5	chr2:62731472..62734976-chr2:62932827..62936526,3	K562	blood:
6	chr2:62731742..62734497-chr2:62931519..62934102,3	MCF-7	breast:

Variant related genes	Relation type
TMEM17	TF binding region
ENSG00000115504	Chromatin interaction
ENSG00000252436	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11678340	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11692210	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12998202	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13035483	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34264648	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36006708	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4075354	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4514865	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66636810	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72805589	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72805590	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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 miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62732200-62733800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:62732200-62733800	Active TSS	Brain Cingulate Gyrus	brain
3	chr2:62732400-62733800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:62732400-62733800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:62732400-62733800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:62732400-62733800	Active TSS	Brain Angular Gyrus	brain
7	chr2:62732400-62733800	Active TSS	Colonic Mucosa	Colon
8	chr2:62732400-62733800	Active TSS	Duodenum Mucosa	Duodenum
9	chr2:62732400-62733800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:62732400-62733800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:62732400-62733800	Active TSS	GM12878-XiMat	blood
12	chr2:62732400-62734000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:62732400-62734000	Active TSS	Brain Substantia Nigra	brain
14	chr2:62732400-62734000	Active TSS	Fetal Brain Female	brain
15	chr2:62732400-62734000	Active TSS	Fetal Kidney	kidney
16	chr2:62732400-62734000	Active TSS	Fetal Thymus	thymus
17	chr2:62732600-62733800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:62732600-62733800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:62732600-62733800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:62732600-62733800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:62732600-62733800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:62732600-62733800	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr2:62732600-62733800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:62732600-62733800	Active TSS	Brain Hippocampus Middle	brain
25	chr2:62732600-62733800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:62732600-62733800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:62732600-62733800	Active TSS	Colon Smooth Muscle	Colon
28	chr2:62732600-62733800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr2:62732600-62733800	Active TSS	Fetal Intestine Small	intestine
30	chr2:62732600-62733800	Active TSS	Fetal Lung	lung
31	chr2:62732600-62733800	Active TSS	Placenta	Placenta
32	chr2:62732600-62733800	Active TSS	Fetal Stomach	stomach
33	chr2:62732600-62733800	Active TSS	Left Ventricle	heart
34	chr2:62732600-62733800	Active TSS	Pancreas	Pancrea
35	chr2:62732600-62733800	Active TSS	Rectal Smooth Muscle	rectum
36	chr2:62732600-62733800	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr2:62732600-62733800	Active TSS	HSMM	muscle
38	chr2:62732600-62733800	Active TSS	NHEK	skin
39	chr2:62732600-62734000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr2:62732600-62734000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:62732600-62734000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:62732600-62734000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:62732600-62734000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:62732600-62734000	Active TSS	Aorta	Aorta
45	chr2:62732600-62734000	Active TSS	Brain Germinal Matrix	brain
46	chr2:62732600-62734000	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr2:62732600-62734000	Active TSS	Fetal Muscle Trunk	muscle
48	chr2:62732600-62734000	Active TSS	Ovary	ovary
49	chr2:62732600-62734000	Active TSS	Psoas Muscle	Psoas
50	chr2:62732600-62734000	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links