Variant report

Variant	rs2056654
Chromosome Location	chr2:39670429-39670430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39669445..39671277-chr2:39681735..39683817,2	K562	blood:
2	chr2:39663101..39666745-chr2:39668624..39671198,3	MCF-7	breast:
3	chr2:39668408..39675131-chr2:39676739..39679699,8	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10169391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.90[AFR][1000 genomes]
rs10170604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.85[AFR][1000 genomes]
rs10175333	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.85[AFR][1000 genomes]
rs10865152	0.85[AFR][1000 genomes]
rs11124677	0.80[AFR][1000 genomes]
rs11124679	0.89[AFR][1000 genomes]
rs11124681	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.86[AFR][1000 genomes]
rs12712641	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474424	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.85[AFR][1000 genomes]
rs2005892	0.84[AFR][1000 genomes]
rs2111382	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160661	1.00[AMR][1000 genomes]
rs2178762	0.88[AFR][1000 genomes]
rs2193422	0.85[AFR][1000 genomes]
rs2373536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.87[AFR][1000 genomes]
rs4670934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.86[AFR][1000 genomes]
rs6544223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6724393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.89[AFR][1000 genomes]
rs6741312	1.00[AMR][1000 genomes]
rs6742170	0.85[AFR][1000 genomes]
rs6759495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.85[AFR][1000 genomes]
rs7578136	0.84[AFR][1000 genomes]
rs7582160	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603392	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7608153	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:39665600-39684200	Weak transcription	Lung	lung
4	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
5	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
7	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39666400-39670600	Weak transcription	Liver	Liver
11	chr2:39666600-39671000	Weak transcription	Right Atrium	heart
12	chr2:39666600-39673000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:39666600-39675800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:39666800-39670800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:39666800-39671400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:39666800-39677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:39666800-39681600	Weak transcription	Ovary	ovary
20	chr2:39667000-39670600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:39667000-39670600	Weak transcription	Aorta	Aorta
22	chr2:39667000-39670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:39667000-39672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
27	chr2:39667200-39672400	Weak transcription	Fetal Stomach	stomach
28	chr2:39667200-39685200	Weak transcription	NHEK	skin
29	chr2:39667200-39694600	Weak transcription	NHLF	lung
30	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
31	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
32	chr2:39667400-39670600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:39667400-39671000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:39667400-39671400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:39667400-39672200	Weak transcription	Brain Anterior Caudate	brain
36	chr2:39667400-39674600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:39667400-39682000	Weak transcription	HSMM	muscle
38	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:39667600-39670800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:39667600-39672800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39667600-39674400	Weak transcription	Osteobl	bone
43	chr2:39667600-39675000	Weak transcription	HMEC	breast
44	chr2:39667800-39674400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:39668200-39670800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:39668200-39671000	Weak transcription	HepG2	liver
47	chr2:39668200-39673600	Weak transcription	Psoas Muscle	Psoas
48	chr2:39668200-39675000	Weak transcription	NH-A	brain
49	chr2:39668200-39681400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:39668200-39684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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