Variant report

Variant	rs55981410
Chromosome Location	chr2:128226112-128226113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128221686..128223814-chr2:128225539..128227819,2	MCF-7	breast:
2	chr2:128223739..128227371-chr2:128227403..128230155,4	K562	blood:
3	chr2:128223739..128227156-chr2:128228484..128231083,5	K562	blood:

Variant related genes	Relation type
ENSG00000202429	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10190872	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10206221	0.81[AMR][1000 genomes]
rs12470481	0.97[ASN][1000 genomes]
rs12475217	0.83[ASN][1000 genomes]
rs12621149	0.82[ASN][1000 genomes]
rs12987418	0.97[ASN][1000 genomes]
rs1549767	0.82[ASN][1000 genomes]
rs17015347	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs173013	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2078028	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2176595	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566564	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2679402	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334139	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334140	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334142	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334147	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334148	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334149	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334150	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334153	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334155	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334162	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732208	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4423553	0.82[AMR][1000 genomes]
rs4662582	0.94[ASN][1000 genomes]
rs56217122	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56234754	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58462277	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59934067	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61342606	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707425	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6722447	0.83[ASN][1000 genomes]
rs6731270	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6748790	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6757654	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72958594	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72958600	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7574209	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7574215	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7576217	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7598346	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7603777	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs777547	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs777549	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs777550	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs777551	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs777557	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs777558	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs777561	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs777562	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs777563	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	esv3693423	chr2:128223875-128230794	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128206200-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:128206800-128233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:128208400-128238800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:128209000-128238000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:128209200-128237600	Weak transcription	Adipose Nuclei	Adipose
6	chr2:128210000-128226400	Weak transcription	Esophagus	oesophagus
7	chr2:128210000-128227200	Weak transcription	Left Ventricle	heart
8	chr2:128210000-128237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:128210200-128238000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:128211400-128226600	Weak transcription	Ovary	ovary
11	chr2:128211600-128226800	Weak transcription	Brain Angular Gyrus	brain
12	chr2:128211600-128227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:128211600-128237600	Weak transcription	Right Ventricle	heart
14	chr2:128212200-128226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:128213000-128237600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:128213200-128237800	Weak transcription	Colonic Mucosa	Colon
17	chr2:128213400-128237800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:128213600-128226600	Weak transcription	Gastric	stomach
19	chr2:128213600-128237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:128213600-128237800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:128213800-128238000	Weak transcription	Brain Germinal Matrix	brain
22	chr2:128215400-128226800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:128216200-128233600	Weak transcription	GM12878-XiMat	blood
24	chr2:128219800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:128220400-128239800	Weak transcription	Fetal Lung	lung
26	chr2:128221400-128226600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:128221600-128226600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:128221600-128226800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:128221600-128227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:128221600-128229000	Weak transcription	HepG2	liver
31	chr2:128221600-128230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:128221600-128237400	Weak transcription	HSMM	muscle
33	chr2:128221600-128237600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:128222200-128237800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:128222400-128237600	Weak transcription	Osteobl	bone
36	chr2:128222400-128237800	Weak transcription	Fetal Brain Female	brain
37	chr2:128222600-128226800	Weak transcription	Fetal Thymus	thymus
38	chr2:128222600-128237000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:128222600-128237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:128222800-128230400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:128222800-128233400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:128222800-128237600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:128222800-128237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:128222800-128239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:128223000-128226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:128223000-128226600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:128223000-128227000	Weak transcription	NHEK	skin
48	chr2:128223000-128227400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:128223000-128237600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:128223200-128237000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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