Variant report

Variant	rs762485
Chromosome Location	chr1:95004084-95004085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:95003840-95004357	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:95003773-95004551	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:95004000-95004150	HVMF	connective:	n/a	n/a
4	CHD2	chr1:95003902-95004179	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr1:95003940-95004090	HFF-Myc	foreskin:	n/a	n/a
6	POLR2A	chr1:94992567-95005960	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:95003452-95004561	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr1:95003857-95004149	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:95003836-95008278	U87	brain:	n/a	n/a
12	CTCF	chr1:95003940-95004090	HFF	foreskin:	n/a	n/a
13	POLR2A	chr1:95002345-95004351	MCF10A-Er-Src	breast:	n/a	n/a
14	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
15	CTCF	chr1:95003940-95004090	NHDF-neo	bronchial:	n/a	n/a
16	CTCF	chr1:95003960-95004110	SAEC	small airway:	n/a	n/a
17	POLR2A	chr1:95003842-95005922	U87	brain:	n/a	n/a
18	SMC3	chr1:95003914-95004158	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr1:95003759-95004169	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:94999692-95008368	ProgFib	skin:	n/a	n/a
21	POLR2A	chr1:95003606-95004559	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr1:95003821-95004120	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95002334..95004389-chr1:95062847..95065293,3	MCF-7	breast:

No data

Variant related genes	Relation type
F3	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1144300	1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1361600	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761955	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3917615	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs841697	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958587	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][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	nsv871764	chr1:94917402-95004084	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94958600-95004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:94972200-95004400	Weak transcription	A549	lung
4	chr1:94979200-95005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:94986000-95006200	Weak transcription	Liver	Liver
6	chr1:94993600-95004800	Weak transcription	HSMMtube	muscle
7	chr1:94994400-95005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:94994600-95005200	Weak transcription	Esophagus	oesophagus
9	chr1:94994600-95006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:94995200-95006200	Weak transcription	Spleen	Spleen
11	chr1:94996800-95005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:94997600-95005000	Weak transcription	Dnd41	blood
13	chr1:94997600-95005200	Weak transcription	Gastric	stomach
14	chr1:94999000-95005400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:95000400-95005600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr1:95001000-95004200	Genic enhancers	HepG2	liver
17	chr1:95001200-95006400	Weak transcription	Small Intestine	intestine
18	chr1:95001400-95006600	Transcr. at gene 5' and 3'	HMEC	breast
19	chr1:95001600-95004600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:95001600-95006200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:95001600-95007400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:95001600-95007800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:95001800-95006000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:95001800-95006200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:95001800-95007000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:95001800-95007800	Active TSS	Brain Hippocampus Middle	brain
27	chr1:95002000-95004400	Transcr. at gene 5' and 3'	NH-A	brain
28	chr1:95002000-95005000	Weak transcription	Fetal Stomach	stomach
29	chr1:95002000-95005400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:95002000-95006200	Weak transcription	Aorta	Aorta
31	chr1:95002200-95004200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:95002200-95005200	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:95002200-95006000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:95002400-95004400	Enhancers	Stomach Mucosa	stomach
35	chr1:95002400-95006600	Transcr. at gene 5' and 3'	NHLF	lung
36	chr1:95002600-95005800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:95002600-95006600	Active TSS	Fetal Brain Female	brain
38	chr1:95002800-95004200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:95002800-95004200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:95002800-95004800	Transcr. at gene 5' and 3'	Hela-S3	cervix
41	chr1:95002800-95005400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:95002800-95005800	Enhancers	Fetal Brain Male	brain
43	chr1:95002800-95006800	Transcr. at gene 5' and 3'	NHEK	skin
44	chr1:95002800-95007200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:95002800-95007600	Active TSS	Brain Anterior Caudate	brain
46	chr1:95003000-95004200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:95003000-95004800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:95003000-95007800	Active TSS	Right Atrium	heart
49	chr1:95003000-95008400	Active TSS	Brain Angular Gyrus	brain
50	chr1:95003200-95006400	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links