Variant report

Variant	rs2054880
Chromosome Location	chr3:156499981-156499982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156497858..156501596-chr3:156502537..156507306,7	K562	blood:
2	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
3	chr3:156487583..156490581-chr3:156498612..156500239,2	MCF-7	breast:
4	chr3:156495724..156497508-chr3:156498193..156500203,2	MCF-7	breast:
5	chr3:156498565..156501614-chr3:156533587..156536301,3	MCF-7	breast:
6	chr3:156390798..156394292-chr3:156499853..156502886,3	MCF-7	breast:
7	chr3:156491310..156495607-chr3:156498419..156501003,3	K562	blood:
8	chr3:156498174..156501165-chr3:156515710..156519959,5	K562	blood:
9	chr3:156498434..156501596-chr3:156502537..156507306,7	K562	blood:
10	chr3:156499863..156500683-chr3:156530309..156531040,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13068223	0.88[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs13070271	0.83[JPT][hapmap]
rs1320011	0.83[JPT][hapmap]
rs1574980	0.83[JPT][hapmap]
rs2874488	0.83[JPT][hapmap]
rs343994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs344022	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs344035	0.85[ASN][1000 genomes]
rs344073	0.83[JPT][hapmap]
rs344079	0.83[JPT][hapmap]
rs344080	0.83[JPT][hapmap]
rs344082	0.83[JPT][hapmap]
rs344084	0.83[JPT][hapmap]
rs344087	0.83[JPT][hapmap]
rs345985	0.80[CHB][hapmap]
rs386736	0.96[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4098	0.89[CHB][hapmap]
rs4315647	0.83[JPT][hapmap]
rs453219	0.83[JPT][hapmap]
rs4680311	0.83[JPT][hapmap]
rs6762708	0.83[JPT][hapmap]
rs6765353	0.83[JPT][hapmap]
rs7638330	0.83[JPT][hapmap]
rs88053	0.83[AFR][1000 genomes]
rs9818684	0.82[CHB][hapmap]
rs9870137	0.83[JPT][hapmap]
rs9876148	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156494600-156510800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:156495400-156500800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:156496200-156501400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:156498800-156501800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:156499000-156500000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:156499000-156500400	Enhancers	Stomach Mucosa	stomach
7	chr3:156499000-156502400	Enhancers	NHDF-Ad	bronchial
8	chr3:156499000-156502400	Enhancers	Osteobl	bone
9	chr3:156499000-156507400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:156499200-156500000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:156499200-156500000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:156499200-156500000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:156499200-156500000	Flanking Active TSS	A549	lung
14	chr3:156499200-156500200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:156499200-156500200	Flanking Active TSS	K562	blood
16	chr3:156499200-156501800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:156499200-156502200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:156499200-156502200	Enhancers	NH-A	brain
19	chr3:156499200-156502400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:156499200-156503200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:156499200-156503200	Enhancers	HUVEC	blood vessel
22	chr3:156499400-156500000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:156499400-156500000	Enhancers	NHLF	lung
24	chr3:156499400-156502200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:156499600-156500000	Flanking Active TSS	Hela-S3	cervix
26	chr3:156499600-156500000	Enhancers	HSMM	muscle
27	chr3:156499600-156504600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:156499800-156500000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:156499800-156500000	Flanking Active TSS	NHEK	skin
30	chr3:156499800-156500200	Genic enhancers	HMEC	breast
31	chr3:156499800-156501400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:156499800-156502000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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