Variant report

Variant	rs1000829
Chromosome Location	chr2:20795182-20795183
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	ZEB1	chr2:20795008-20795650	GM12878	blood:	n/a	n/a
2	RCOR1	chr2:20794926-20796101	GM12878	blood:	n/a	n/a
3	POU2F2	chr2:20795167-20795952	GM12878	blood:	n/a	chr2:20795447-20795469 chr2:20795454-20795464 chr2:20795454-20795464 chr2:20795453-20795465 chr2:20795455-20795462 chr2:20795451-20795466 chr2:20795451-20795465 chr2:20795454-20795463
4	MEF2C	chr2:20795096-20795960	GM12878	blood:	n/a	chr2:20795435-20795443
5	POLR2A	chr2:20795002-20796171	GM12891	blood:	n/a	n/a
6	TAF1	chr2:20795129-20795580	GM12878	blood:	n/a	n/a
7	YY1	chr2:20795141-20795977	GM12878	blood:	n/a	chr2:20795382-20795404
8	BCL11A	chr2:20795157-20796071	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:20795052-20795989	GM12891	blood:	n/a	n/a
10	SP1	chr2:20795158-20796053	GM12878	blood:	n/a	chr2:20795176-20795190
11	IRF3	chr2:20795150-20795350	GM12878	blood:	n/a	n/a
12	RELA	chr2:20794814-20796033	GM10847	blood:	n/a	n/a
13	YY1	chr2:20795090-20795830	GM12892	blood:	n/a	chr2:20795382-20795404
14	PML	chr2:20795155-20795629	GM12878	blood:	n/a	n/a
15	RFX5	chr2:20795079-20795581	GM12878	blood:	n/a	n/a
16	BCLAF1	chr2:20795035-20796067	GM12878	blood:	n/a	n/a
17	CBX3	chr2:20795041-20796175	K562	blood:	n/a	n/a
18	PML	chr2:20794992-20796252	GM12878	blood:	n/a	n/a
19	RELA	chr2:20795043-20796237	GM19099	blood:	n/a	n/a
20	POLR2A	chr2:20795121-20795746	GM12878	blood:	n/a	n/a
21	BCL11A	chr2:20795139-20795600	GM12878	blood:	n/a	n/a
22	MXI1	chr2:20795121-20796144	GM12878	blood:	n/a	n/a
23	STAT1	chr2:20795158-20795912	GM12878	blood:	n/a	chr2:20795900-20795912 chr2:20795532-20795544
24	NFIC	chr2:20795087-20796145	GM12878	blood:	n/a	n/a
25	E2F4	chr2:20795172-20795347	GM12878	blood:	n/a	n/a
26	POU2F2	chr2:20795054-20796102	GM12878	blood:	n/a	chr2:20795447-20795469 chr2:20795454-20795464 chr2:20795454-20795464 chr2:20795453-20795465 chr2:20795455-20795462 chr2:20795451-20795466 chr2:20795451-20795465 chr2:20795454-20795463
27	POLR2A	chr2:20795025-20796124	GM12878	blood:	n/a	n/a
28	ZNF143	chr2:20795071-20796419	GM12878	blood:	n/a	chr2:20795525-20795543
29	POLR2A	chr2:20795052-20796005	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:20795106-20795753	GM19193	blood:	n/a	n/a
31	NR2F2	chr2:20795020-20796228	K562	blood:	n/a	chr2:20795628-20795643
32	IRF4	chr2:20795065-20796082	GM12878	blood:	n/a	n/a
33	TBP	chr2:20795135-20796073	GM12878	blood:	n/a	n/a
34	MAX	chr2:20795108-20796060	K562	blood:	n/a	chr2:20795679-20795688
35	PAX5	chr2:20795149-20795714	GM12878	blood:	n/a	chr2:20795677-20795695
36	STAT5A	chr2:20794804-20796454	GM12878	blood:	n/a	chr2:20795134-20795142 chr2:20795900-20795912 chr2:20795532-20795544
37	RELA	chr2:20795106-20796552	GM18505	blood:	n/a	n/a
38	EBF1	chr2:20794957-20796053	GM12878	blood:	n/a	chr2:20795594-20795605 chr2:20795237-20795247
39	PAX5	chr2:20795085-20795985	GM12878	blood:	n/a	chr2:20795677-20795695
40	POLR2A	chr2:20795091-20795831	GM12878	blood:	n/a	n/a
41	CHD1	chr2:20794887-20795821	GM12878	blood:	n/a	n/a
42	RUNX3	chr2:20794905-20796091	GM12878	blood:	n/a	n/a
43	SP1	chr2:20795133-20796077	GM12878	blood:	n/a	chr2:20795176-20795190
44	RCOR1	chr2:20795132-20796087	K562	blood:	n/a	n/a
45	PAX5	chr2:20795166-20795582	GM12891	blood:	n/a	n/a
46	NFATC1	chr2:20795056-20795993	GM12878	blood:	n/a	n/a
47	BCLAF1	chr2:20795088-20796207	GM12878	blood:	n/a	n/a
48	MTA3	chr2:20794831-20796689	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:20795031-20796046	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:20795145-20795853	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20666213..20668504-chr2:20794709..20797277,2	MCF-7	breast:
2	chr2:20793781..20795387-chr2:20795652..20798532,2	K562	blood:
3	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
4	chr2:20737451..20739209-chr2:20794150..20795767,2	K562	blood:
5	chr2:20767266..20769028-chr2:20793726..20796533,2	K562	blood:
6	chr2:20784163..20786583-chr2:20792834..20795600,2	MCF-7	breast:
7	chr2:20794523..20801165-chr2:20801395..20807064,11	K562	blood:
8	chr2:20790147..20792298-chr2:20794346..20796797,2	K562	blood:
9	chr2:20767266..20769707-chr2:20793726..20796533,3	K562	blood:
10	chr2:20689974..20693202-chr2:20793219..20795538,3	MCF-7	breast:
11	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:

Variant related genes	Relation type
HS1BP3-IT1	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000233416	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1000830	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11885770	1.00[EUR][1000 genomes]
rs13013492	1.00[EUR][1000 genomes]
rs4666448	1.00[EUR][1000 genomes]
rs6531250	1.00[EUR][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	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:20785800-20795200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
4	chr2:20786000-20795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
6	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
7	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:20789200-20797000	Enhancers	Spleen	Spleen
9	chr2:20789200-20800400	Enhancers	Placenta	Placenta
10	chr2:20789400-20795400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:20790200-20797800	Enhancers	Fetal Intestine Large	intestine
12	chr2:20790800-20801200	Enhancers	Adipose Nuclei	Adipose
13	chr2:20791200-20795200	Weak transcription	Esophagus	oesophagus
14	chr2:20791200-20795400	Weak transcription	Fetal Brain Male	brain
15	chr2:20791200-20795600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:20791200-20796600	Weak transcription	Fetal Heart	heart
17	chr2:20791400-20796600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:20791800-20796400	Weak transcription	Pancreas	Pancrea
19	chr2:20791800-20797200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:20791800-20800400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:20792000-20797800	Enhancers	HSMM	muscle
22	chr2:20792000-20798200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:20792200-20797800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:20792200-20797800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:20792200-20797800	Enhancers	NH-A	brain
26	chr2:20792200-20798200	Enhancers	Ovary	ovary
27	chr2:20792400-20797600	Enhancers	A549	lung
28	chr2:20792400-20797800	Enhancers	Lung	lung
29	chr2:20792400-20797800	Enhancers	NHLF	lung
30	chr2:20792400-20798400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:20792400-20800200	Enhancers	Right Atrium	heart
32	chr2:20792600-20797200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr2:20792600-20797800	Enhancers	NHDF-Ad	bronchial
34	chr2:20792800-20797200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:20792800-20798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:20792800-20801800	Enhancers	HUVEC	blood vessel
37	chr2:20793000-20795200	Weak transcription	Colonic Mucosa	Colon
38	chr2:20793000-20795400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:20793000-20797800	Enhancers	Brain Hippocampus Middle	brain
40	chr2:20793000-20799000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr2:20793000-20800400	Enhancers	Left Ventricle	heart
42	chr2:20793000-20801200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:20793200-20795400	Weak transcription	Fetal Kidney	kidney
44	chr2:20793200-20795600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr2:20793200-20796200	Enhancers	Liver	Liver
46	chr2:20793400-20795200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:20793400-20796200	Weak transcription	Fetal Lung	lung
48	chr2:20793400-20797600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:20793600-20795200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:20793600-20797400	Enhancers	Primary B cells from peripheral blood	blood

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