Variant report

Variant	rs2560774
Chromosome Location	chr6:13527533-13527534
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13523078..13528567-chr6:13572959..13576229,4	MCF-7	breast:
2	chr6:13474713..13477366-chr6:13526684..13528787,2	MCF-7	breast:
3	chr6:13527086..13529116-chr6:13531741..13533503,2	K562	blood:
4	chr6:13527340..13529081-chr6:13533634..13535711,2	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs2081874	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2434397	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2434398	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494775	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560764	0.92[EUR][1000 genomes]
rs2560767	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560775	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560776	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560777	0.93[ASN][1000 genomes]
rs2560778	0.93[ASN][1000 genomes]
rs2560780	0.93[ASN][1000 genomes]
rs2560781	0.93[ASN][1000 genomes]
rs2560784	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560786	0.89[ASN][1000 genomes]
rs2560787	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560789	0.91[ASN][1000 genomes]
rs2560790	0.91[ASN][1000 genomes]
rs2560791	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560793	0.91[ASN][1000 genomes]
rs2560794	0.88[ASN][1000 genomes]
rs2560796	0.91[ASN][1000 genomes]
rs2560797	0.91[ASN][1000 genomes]
rs2560798	0.90[ASN][1000 genomes]
rs2560799	0.88[ASN][1000 genomes]
rs2560800	0.81[ASN][1000 genomes]
rs2560802	0.89[ASN][1000 genomes]
rs2560804	0.89[ASN][1000 genomes]
rs2560805	0.89[ASN][1000 genomes]
rs2560806	0.89[ASN][1000 genomes]
rs2841504	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2841526	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841527	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841530	0.92[ASN][1000 genomes]
rs2841531	0.88[ASN][1000 genomes]
rs2841532	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2841533	0.91[ASN][1000 genomes]
rs2841535	0.91[ASN][1000 genomes]
rs2841536	0.90[ASN][1000 genomes]
rs2841537	0.91[ASN][1000 genomes]
rs2841540	0.91[ASN][1000 genomes]
rs2841542	0.89[ASN][1000 genomes]
rs2841543	0.89[ASN][1000 genomes]
rs2841544	0.89[ASN][1000 genomes]
rs2841545	0.89[ASN][1000 genomes]
rs2841569	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841570	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841572	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4340988	0.93[ASN][1000 genomes]
rs4512205	0.93[ASN][1000 genomes]
rs4715370	0.91[ASN][1000 genomes]
rs4715371	0.91[ASN][1000 genomes]
rs4715372	0.91[ASN][1000 genomes]
rs4715373	0.93[ASN][1000 genomes]
rs4715374	0.93[ASN][1000 genomes]
rs4715376	0.88[ASN][1000 genomes]
rs4715379	0.99[ASN][1000 genomes]
rs4715380	0.99[ASN][1000 genomes]
rs4715388	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59610068	0.91[ASN][1000 genomes]
rs60499941	0.91[ASN][1000 genomes]
rs61312460	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62387366	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62387367	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62387368	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62387369	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458898	0.97[ASN][1000 genomes]
rs6923024	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939496	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73723737	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7763316	0.87[ASN][1000 genomes]
rs9370167	0.91[ASN][1000 genomes]
rs9370168	0.91[ASN][1000 genomes]
rs9370171	0.91[ASN][1000 genomes]
rs9370172	0.90[ASN][1000 genomes]
rs9370202	0.87[ASN][1000 genomes]
rs9382156	0.89[ASN][1000 genomes]
rs9382170	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382172	0.91[ASN][1000 genomes]
rs9382174	0.88[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13521600-13529200	Enhancers	HUVEC	blood vessel
2	chr6:13523000-13530000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:13523800-13527800	Enhancers	Fetal Thymus	thymus
4	chr6:13524000-13528200	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:13524000-13528200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:13524000-13530000	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:13524800-13527600	Weak transcription	Spleen	Spleen
8	chr6:13524800-13529000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:13525000-13529000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13525200-13528200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr6:13525200-13529000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:13525200-13532400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:13525200-13534800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:13525600-13528200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:13525600-13528200	Enhancers	Primary B cells from cord blood	blood
16	chr6:13525800-13527600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:13525800-13528200	Enhancers	Adipose Nuclei	Adipose
18	chr6:13526000-13527600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:13526000-13527800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:13526000-13530000	Enhancers	Fetal Brain Male	brain
21	chr6:13526200-13527600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:13526200-13527800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:13526200-13527800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:13526200-13527800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:13526200-13528000	Enhancers	Placenta	Placenta
26	chr6:13526200-13528200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:13526400-13527600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:13526400-13527600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:13526400-13527600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr6:13526400-13527600	Enhancers	GM12878-XiMat	blood
31	chr6:13526400-13527600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:13526600-13527600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:13526600-13527600	Enhancers	Brain Hippocampus Middle	brain
34	chr6:13526600-13527600	Enhancers	Fetal Brain Female	brain
35	chr6:13526600-13527600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:13526600-13527800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:13526600-13529800	Enhancers	Fetal Heart	heart
38	chr6:13526800-13527600	Enhancers	Duodenum Mucosa	Duodenum
39	chr6:13526800-13527600	Enhancers	Fetal Muscle Leg	muscle
40	chr6:13526800-13527600	Enhancers	Left Ventricle	heart
41	chr6:13526800-13527600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr6:13526800-13527600	Enhancers	Small Intestine	intestine
43	chr6:13526800-13527800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:13526800-13527800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr6:13526800-13528200	Enhancers	HSMMtube	muscle
46	chr6:13526800-13528200	Enhancers	NHEK	skin
47	chr6:13527000-13527600	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:13527000-13528000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:13527200-13527600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:13527200-13527600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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