Variant report

Variant	rs169172
Chromosome Location	chr1:70689677-70689678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70689433-70690393	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:70686388-70698918	K562	blood:	n/a	n/a
3	POLR2A	chr1:70689625-70691541	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70669146..70671967-chr1:70689438..70693050,5	K562	blood:
2	chr1:70688424..70691720-chr1:70692048..70694571,6	MCF-7	breast:
3	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
4	chr1:70667153..70674800-chr1:70681943..70693478,26	K562	blood:
5	chr1:70685268..70690578-chr1:70702989..70707451,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228988	TF binding region
SRSF11	TF binding region
ENSG00000066557	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs574587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs595662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs647872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690916	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs699221	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72678626	0.82[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	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv871898	chr1:70681486-70723347	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70687800-70691200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:70687800-70697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:70687800-70698600	Weak transcription	Gastric	stomach
4	chr1:70687800-70698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:70687800-70699600	Weak transcription	Lung	lung
6	chr1:70687800-70699600	Weak transcription	Spleen	Spleen
7	chr1:70688000-70689800	Weak transcription	Left Ventricle	heart
8	chr1:70688000-70690000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:70688000-70690000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:70688000-70697200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:70688000-70697200	Weak transcription	Pancreas	Pancrea
12	chr1:70688000-70697800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:70688000-70699000	Weak transcription	Psoas Muscle	Psoas
14	chr1:70688000-70710400	Weak transcription	Aorta	Aorta
15	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
16	chr1:70688200-70689800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:70688200-70689800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:70688200-70690000	Enhancers	Brain Substantia Nigra	brain
19	chr1:70688200-70690600	Weak transcription	Thymus	Thymus
20	chr1:70688200-70696200	Weak transcription	Colonic Mucosa	Colon
21	chr1:70688200-70708200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:70688400-70689800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
23	chr1:70688400-70689800	Enhancers	Brain Hippocampus Middle	brain
24	chr1:70688400-70689800	Enhancers	Fetal Intestine Small	intestine
25	chr1:70688400-70689800	Transcr. at gene 5' and 3'	K562	blood
26	chr1:70688400-70690000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:70688400-70693000	Weak transcription	Fetal Stomach	stomach
28	chr1:70688400-70693800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:70688400-70719400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:70688600-70689800	Transcr. at gene 5' and 3'	NHLF	lung
31	chr1:70688600-70690000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:70688600-70691400	Genic enhancers	Colon Smooth Muscle	Colon
33	chr1:70688600-70691800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:70688600-70719800	Strong transcription	Fetal Thymus	thymus
35	chr1:70688800-70689800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:70688800-70689800	Enhancers	Primary T cells from cord blood	blood
37	chr1:70688800-70690000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:70688800-70690200	Genic enhancers	Primary hematopoietic stem cells	blood
39	chr1:70688800-70690400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr1:70688800-70690400	Genic enhancers	Fetal Lung	lung
41	chr1:70688800-70690800	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr1:70688800-70691000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:70688800-70691000	Genic enhancers	Liver	Liver
44	chr1:70688800-70691200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
45	chr1:70688800-70691600	Strong transcription	HSMM	muscle
46	chr1:70688800-70692400	Weak transcription	Right Atrium	heart
47	chr1:70688800-70692600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:70689000-70689800	Genic enhancers	Rectal Smooth Muscle	rectum
49	chr1:70689000-70690000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:70689000-70690000	Genic enhancers	Primary B cells from cord blood	blood

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