Variant report

Variant	rs12989854
Chromosome Location	chr2:55381538-55381539
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
2	chr2:55276755..55278811-chr2:55380705..55382664,2	K562	blood:
3	chr2:55381461..55384180-chr2:55385114..55387794,2	MCF-7	breast:
4	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1134722	0.84[EUR][1000 genomes]
rs11686766	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686912	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687876	0.84[EUR][1000 genomes]
rs12995548	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13000786	0.84[EUR][1000 genomes]
rs13003020	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13012567	0.84[EUR][1000 genomes]
rs13014752	0.84[EUR][1000 genomes]
rs13017468	0.84[EUR][1000 genomes]
rs2028139	0.86[EUR][1000 genomes]
rs34447956	0.84[EUR][1000 genomes]
rs35141050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183885	0.86[EUR][1000 genomes]
rs35227659	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297827	0.83[EUR][1000 genomes]
rs35700883	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121000	0.84[EUR][1000 genomes]
rs4318424	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627623	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742306	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6743339	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6747466	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414544	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414545	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414546	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414548	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71414549	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs71414556	0.84[EUR][1000 genomes]
rs71414557	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55371600-55382400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:55376800-55382000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:55376800-55382400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:55377400-55381800	Enhancers	GM12878-XiMat	blood
6	chr2:55377400-55382000	Enhancers	Primary B cells from cord blood	blood
7	chr2:55377600-55381800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:55378200-55382400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:55378200-55383600	Enhancers	Brain Substantia Nigra	brain
12	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
13	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
15	chr2:55378400-55381800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr2:55378400-55383800	Enhancers	NHLF	lung
17	chr2:55378600-55383200	Enhancers	Colon Smooth Muscle	Colon
18	chr2:55378600-55383600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
22	chr2:55378800-55382000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:55378800-55382600	Enhancers	Placenta	Placenta
24	chr2:55378800-55383200	Enhancers	Fetal Brain Male	brain
25	chr2:55378800-55383600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:55379000-55382000	Weak transcription	Left Ventricle	heart
29	chr2:55379000-55384200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:55379200-55383000	Enhancers	Fetal Brain Female	brain
31	chr2:55379200-55383600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:55379200-55385200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:55379400-55381800	Enhancers	Small Intestine	intestine
34	chr2:55379400-55385200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:55379400-55386600	Enhancers	Fetal Intestine Large	intestine
36	chr2:55379400-55387000	Enhancers	Fetal Intestine Small	intestine
37	chr2:55379600-55382200	Enhancers	K562	blood
38	chr2:55379600-55385000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:55379600-55386800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:55380000-55384400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:55380200-55381600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:55380200-55382000	Weak transcription	Psoas Muscle	Psoas
43	chr2:55380200-55382600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:55380200-55386000	Enhancers	Hela-S3	cervix
45	chr2:55380400-55384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:55380600-55381600	Enhancers	Fetal Lung	lung
47	chr2:55380600-55383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:55380600-55384000	Enhancers	Fetal Heart	heart
49	chr2:55380600-55384000	Enhancers	HMEC	breast
50	chr2:55380800-55381800	Flanking Active TSS	NHEK	skin

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