Variant report

Variant	rs2787921
Chromosome Location	chr6:88400512-88400513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88392656..88394739-chr6:88399479..88401208,2	K562	blood:
2	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:
3	chr6:88399461..88401645-chr6:88409406..88411784,2	MCF-7	breast:
4	chr6:88395462..88397221-chr6:88400154..88401972,2	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10755484	0.85[EUR][1000 genomes]
rs13193380	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13194003	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246113	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2307379	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2325064	0.83[EUR][1000 genomes]
rs2754247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2754248	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2754262	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754264	0.83[EUR][1000 genomes]
rs2787893	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2787924	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2787934	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2814712	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757368	0.83[EUR][1000 genomes]
rs3934838	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4334949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4464759	0.89[EUR][1000 genomes]
rs4498321	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4587138	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4587143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4706294	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707373	0.84[EUR][1000 genomes]
rs4707374	0.88[EUR][1000 genomes]
rs4707376	0.90[EUR][1000 genomes]
rs4707377	0.90[EUR][1000 genomes]
rs4707379	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4707382	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707383	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454632	0.86[EUR][1000 genomes]
rs6454636	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454638	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454640	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454641	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906769	0.86[EUR][1000 genomes]
rs6908386	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6916732	0.89[EUR][1000 genomes]
rs6918909	0.83[EUR][1000 genomes]
rs6928160	0.87[EUR][1000 genomes]
rs6930600	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931069	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6940150	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7741825	0.80[ASN][1000 genomes]
rs7742965	0.90[EUR][1000 genomes]
rs7746465	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7750207	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7752494	0.80[EUR][1000 genomes]
rs7755167	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7757636	0.89[EUR][1000 genomes]
rs7757794	0.88[EUR][1000 genomes]
rs7762864	0.86[EUR][1000 genomes]
rs7772561	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773906	0.87[EUR][1000 genomes]
rs9444512	0.82[EUR][1000 genomes]
rs9444519	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9444522	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9444524	0.90[EUR][1000 genomes]
rs9444525	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444526	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444530	0.81[ASN][1000 genomes]
rs9450723	0.83[EUR][1000 genomes]
rs9450732	0.87[EUR][1000 genomes]
rs9450733	0.87[EUR][1000 genomes]
rs9450738	0.90[EUR][1000 genomes]
rs9450739	0.90[EUR][1000 genomes]
rs9450744	0.90[EUR][1000 genomes]
rs9450752	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450755	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450762	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
4	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
5	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
6	chr6:88387800-88400600	Weak transcription	K562	blood
7	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
8	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
10	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
11	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
13	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain
21	chr6:88391400-88400800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:88392000-88401200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:88392200-88405200	Weak transcription	Fetal Brain Male	brain
24	chr6:88392400-88400600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:88392400-88400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:88392400-88401400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
30	chr6:88392600-88406800	Weak transcription	HSMM	muscle
31	chr6:88392600-88407200	Weak transcription	HMEC	breast
32	chr6:88393000-88401200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:88393000-88401400	Weak transcription	NHEK	skin
34	chr6:88393600-88402600	Weak transcription	Esophagus	oesophagus
35	chr6:88393600-88404000	Weak transcription	HUVEC	blood vessel
36	chr6:88393800-88405600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:88394000-88401200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:88394600-88401400	Weak transcription	Primary T cells from cord blood	blood
39	chr6:88394800-88402200	Enhancers	Adipose Nuclei	Adipose
40	chr6:88395000-88407200	Weak transcription	Hela-S3	cervix
41	chr6:88395200-88400600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:88395200-88401400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:88395400-88401400	Weak transcription	Brain Angular Gyrus	brain
44	chr6:88395600-88401400	Weak transcription	Fetal Lung	lung
45	chr6:88396200-88401200	Weak transcription	Brain Substantia Nigra	brain
46	chr6:88396200-88401400	Weak transcription	Fetal Intestine Large	intestine
47	chr6:88396200-88401800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:88396400-88405200	Weak transcription	Stomach Mucosa	stomach
49	chr6:88396600-88402200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:88397000-88402400	Enhancers	Skeletal Muscle Female	skeletal muscle

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