Variant report

Variant	rs316644
Chromosome Location	chr1:84765831-84765832
allele	A/G
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	MAX	chr1:84763758-84766002	HCT-116	colon:	n/a	n/a
2	GATA3	chr1:84765545-84765834	SH-SY5Y	brain:	n/a	chr1:84765581-84765591
3	EGR1	chr1:84763928-84765913	HCT-116	colon:	n/a	chr1:84764139-84764163 chr1:84764290-84764303 chr1:84765200-84765214 chr1:84764438-84764448 chr1:84765181-84765195 chr1:84765148-84765162 chr1:84764435-84764448
4	TCF7L2	chr1:84765474-84765967	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84765808..84767323-chr1:84944913..84947326,2	K562	blood:
2	chr1:84764306..84766033-chr1:84791086..84793194,2	MCF-7	breast:
3	chr1:84763327..84765739-chr1:84765755..84771723,8	K562	blood:
4	chr1:84765283..84767308-chr1:84944913..84946542,2	K562	blood:

Variant related genes	Relation type
SAMD13	TF binding region
ENSG00000117133	Chromatin interaction
ENSG00000203943	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12037040	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041053	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246550	0.86[CHD][hapmap];0.91[MEX][hapmap]
rs12564352	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690702	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs170278	1.00[YRI][hapmap]
rs184358	0.98[ASN][1000 genomes]
rs315520	1.00[YRI][hapmap]
rs315522	0.82[AFR][1000 genomes]
rs315523	0.82[AFR][1000 genomes]
rs315525	0.81[CHD][hapmap];0.82[YRI][hapmap]
rs315526	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs315527	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs315530	0.81[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs315546	0.82[AFR][1000 genomes]
rs315548	0.82[AFR][1000 genomes]
rs315555	0.81[CHD][hapmap]
rs316637	0.98[ASN][1000 genomes]
rs316639	0.92[ASN][1000 genomes]
rs316643	0.93[ASN][1000 genomes]
rs316660	0.81[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs316661	0.81[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs316663	0.81[CHD][hapmap];0.92[MEX][hapmap]
rs316665	0.82[AFR][1000 genomes]
rs511087	0.82[AFR][1000 genomes]
rs58205457	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698676	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs784832	0.99[ASN][1000 genomes]
rs784833	0.99[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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84762000-84766000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:84763200-84769400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:84764400-84766200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr1:84764800-84766000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:84764800-84770200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:84765000-84767000	Weak transcription	Ovary	ovary
7	chr1:84765200-84766000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:84765200-84766200	Weak transcription	Aorta	Aorta
9	chr1:84765200-84766200	Enhancers	Brain Angular Gyrus	brain
10	chr1:84765200-84766400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:84765200-84766400	Weak transcription	Spleen	Spleen
12	chr1:84765200-84766400	Enhancers	HUVEC	blood vessel
13	chr1:84765200-84766600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:84765200-84766600	Enhancers	Esophagus	oesophagus
15	chr1:84765200-84766600	Weak transcription	Fetal Brain Female	brain
16	chr1:84765200-84766600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:84765200-84766600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:84765200-84766800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:84765200-84766800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:84765200-84766800	Enhancers	Primary T cells from cord blood	blood
21	chr1:84765200-84766800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:84765200-84766800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:84765200-84766800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:84765200-84766800	Enhancers	Colon Smooth Muscle	Colon
25	chr1:84765200-84766800	Enhancers	NH-A	brain
26	chr1:84765200-84767000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:84765200-84767000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:84765200-84767000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:84765200-84767000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:84765200-84767000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:84765200-84767000	Enhancers	Fetal Heart	heart
32	chr1:84765200-84767000	Enhancers	Fetal Stomach	stomach
33	chr1:84765200-84767000	Enhancers	HMEC	breast
34	chr1:84765200-84767000	Weak transcription	HSMMtube	muscle
35	chr1:84765200-84767200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:84765200-84767200	Enhancers	Fetal Thymus	thymus
37	chr1:84765200-84767200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:84765200-84767800	Weak transcription	Left Ventricle	heart
39	chr1:84765200-84768200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:84765200-84768200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:84765400-84766200	Enhancers	Brain Substantia Nigra	brain
42	chr1:84765400-84766200	Weak transcription	Fetal Brain Male	brain
43	chr1:84765400-84766200	Weak transcription	Right Atrium	heart
44	chr1:84765400-84766200	Enhancers	Stomach Smooth Muscle	stomach
45	chr1:84765400-84766400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:84765400-84766400	Enhancers	Fetal Muscle Leg	muscle
47	chr1:84765400-84766400	Enhancers	Dnd41	blood
48	chr1:84765400-84766600	Enhancers	Brain Anterior Caudate	brain
49	chr1:84765400-84766600	Enhancers	Stomach Mucosa	stomach
50	chr1:84765400-84766800	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links