Variant report

Variant	rs2647497
Chromosome Location	chr1:77955556-77955557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77953880..77956106-chr1:78468931..78470595,2	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12731121	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12732561	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12733666	0.82[CEU][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs12746354	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12751064	1.00[CHD][hapmap]
rs12756133	0.85[EUR][1000 genomes]
rs12760589	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13376422	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17380852	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17381664	1.00[CHD][hapmap]
rs1909202	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs1909203	0.91[ASW][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2454328	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2647496	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35254623	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35635429	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35883964	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949662	1.00[CHD][hapmap]
rs4949803	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66538606	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6678622	1.00[CHD][hapmap]
rs6684022	1.00[CHD][hapmap]
rs67045981	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72681697	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77913200-77968400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:77914600-77955600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77935600-77955800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:77940200-77955800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:77940600-77955600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:77940600-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:77945400-77958600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:77945800-77961600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:77953400-77955600	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr1:77954200-77956800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:77954400-77955800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:77954400-77955800	Enhancers	HSMM	muscle
13	chr1:77954400-77956200	Enhancers	HSMMtube	muscle
14	chr1:77954800-77955600	Enhancers	Brain Anterior Caudate	brain
15	chr1:77954800-77955600	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:77954800-77956200	Enhancers	Brain Angular Gyrus	brain
17	chr1:77954800-77956200	Enhancers	Fetal Muscle Leg	muscle
18	chr1:77954800-77956200	Genic enhancers	NHDF-Ad	bronchial
19	chr1:77954800-77956400	Enhancers	Brain Hippocampus Middle	brain
20	chr1:77954800-77956400	Enhancers	Fetal Brain Female	brain
21	chr1:77954800-77958600	Enhancers	Brain Substantia Nigra	brain
22	chr1:77955000-77956600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:77955000-77956800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:77955200-77956000	Enhancers	NH-A	brain
25	chr1:77955200-77956200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:77955400-77956000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:77955400-77956000	Enhancers	NHLF	lung
28	chr1:77955400-77956200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:77955400-77956200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:77955400-77956200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:77955400-77956200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:77955400-77956200	Enhancers	Fetal Kidney	kidney
33	chr1:77955400-77956400	Enhancers	Brain Germinal Matrix	brain
34	chr1:77955400-77956600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:77955400-77956800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:77955400-77956800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:77955400-77958200	Enhancers	Fetal Brain Male	brain

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