Variant report

Variant	rs12564604
Chromosome Location	chr1:77955105-77955106
allele	A/G
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: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11800652	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs11810135	1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs12564592	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12568374	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs12568376	1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs12569104	1.00[CEU][hapmap]
rs17100791	1.00[CEU][hapmap]
rs17100850	1.00[CEU][hapmap]
rs2245189	0.82[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270539	1.00[CEU][hapmap]
rs2291689	1.00[CEU][hapmap]
rs2291690	1.00[CEU][hapmap]
rs2647496	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4949655	0.92[JPT][hapmap]
rs58143971	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58397190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58958142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59076612	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59623467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59913458	0.82[EUR][1000 genomes]
rs60207382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61080952	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61575581	0.82[EUR][1000 genomes]
rs6664497	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6680677	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs74090603	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74090608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74090614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74090617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74090618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74090619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74092662	0.82[EUR][1000 genomes];0.83[ASN][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:29 , 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	chr1:77934600-77955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:77935600-77955800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:77940200-77955800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:77940400-77955400	Weak transcription	NHLF	lung
7	chr1:77940600-77955600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:77940600-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:77940800-77955400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:77944800-77955400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:77945400-77958600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:77945800-77961600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:77953400-77955600	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr1:77954200-77955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:77954200-77955400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:77954200-77956800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:77954400-77955800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:77954400-77955800	Enhancers	HSMM	muscle
19	chr1:77954400-77956200	Enhancers	HSMMtube	muscle
20	chr1:77954800-77955600	Enhancers	Brain Anterior Caudate	brain
21	chr1:77954800-77955600	Enhancers	Brain Cingulate Gyrus	brain
22	chr1:77954800-77956200	Enhancers	Brain Angular Gyrus	brain
23	chr1:77954800-77956200	Enhancers	Fetal Muscle Leg	muscle
24	chr1:77954800-77956200	Genic enhancers	NHDF-Ad	bronchial
25	chr1:77954800-77956400	Enhancers	Brain Hippocampus Middle	brain
26	chr1:77954800-77956400	Enhancers	Fetal Brain Female	brain
27	chr1:77954800-77958600	Enhancers	Brain Substantia Nigra	brain
28	chr1:77955000-77956600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:77955000-77956800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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