Variant report

Variant	rs56234754
Chromosome Location	chr2:128229855-128229856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128220774..128223723-chr2:128228116..128231015,2	K562	blood:
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
ENSG00000231731	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10190872	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10206221	0.87[AMR][1000 genomes]
rs12470481	0.99[ASN][1000 genomes]
rs12475217	0.85[ASN][1000 genomes]
rs12621149	0.83[ASN][1000 genomes]
rs12987418	0.99[ASN][1000 genomes]
rs1549767	0.83[ASN][1000 genomes]
rs17015347	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs173013	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17522960	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2078028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2176595	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2566564	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679402	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334139	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334140	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334147	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334148	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334149	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334150	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334153	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334155	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334162	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732208	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4423553	0.82[AMR][1000 genomes]
rs4662582	0.92[ASN][1000 genomes]
rs55981410	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56217122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58462277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59934067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61342606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707425	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6722447	0.85[ASN][1000 genomes]
rs6731270	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6748790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757654	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958594	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72958600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7574209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574215	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7576217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7598346	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7603777	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777547	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777549	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777550	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777551	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777557	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777558	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777561	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs777562	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs777563	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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:106 , 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	chr2:128210000-128237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:128210200-128238000	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:128211600-128237600	Weak transcription	Right Ventricle	heart
9	chr2:128213000-128237600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:128213200-128237800	Weak transcription	Colonic Mucosa	Colon
11	chr2:128213400-128237800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:128213600-128237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:128213600-128237800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:128213800-128238000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:128216200-128233600	Weak transcription	GM12878-XiMat	blood
16	chr2:128219800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:128220400-128239800	Weak transcription	Fetal Lung	lung
18	chr2:128221600-128230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:128221600-128237400	Weak transcription	HSMM	muscle
20	chr2:128221600-128237600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:128222200-128237800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:128222400-128237600	Weak transcription	Osteobl	bone
23	chr2:128222400-128237800	Weak transcription	Fetal Brain Female	brain
24	chr2:128222600-128237000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:128222600-128237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:128222800-128230400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:128222800-128233400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:128222800-128237600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:128222800-128237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:128222800-128239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:128223000-128237600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:128223200-128237000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:128223200-128237000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:128223200-128237600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:128223200-128237600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:128223200-128237800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:128223200-128237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:128223400-128237000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:128223800-128238400	Weak transcription	K562	blood
41	chr2:128224000-128241800	Weak transcription	Small Intestine	intestine
42	chr2:128224600-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:128224800-128237600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:128225800-128233400	Weak transcription	HUVEC	blood vessel
45	chr2:128226200-128244000	Weak transcription	Psoas Muscle	Psoas
46	chr2:128227400-128233000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:128227400-128233000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:128227400-128237800	Weak transcription	Primary B cells from cord blood	blood
49	chr2:128227400-128237800	Weak transcription	A549	lung
50	chr2:128227400-128238800	Weak transcription	Ovary	ovary

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