Variant report

Variant	rs55831980
Chromosome Location	chr2:9898350-9898351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9891910..9893733-chr2:9895279..9898420,3	MCF-7	breast:
2	chr2:9897830..9899713-chr2:9900837..9903744,2	K562	blood:
3	chr2:9891163..9893022-chr2:9896031..9898454,2	K562	blood:
4	chr2:9897337..9900295-chr2:9937034..9939837,3	K562	blood:
5	chr2:9897831..9899412-chr2:9902196..9904626,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YWHAQ-1	chr2:9897625-9899428	XLOC_001982

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10189991	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11889675	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12329266	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12619723	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13393165	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13406396	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13412895	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16867150	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16867153	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16867155	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4145374	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55683574	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67071207	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67169917	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72779090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72779094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9892400-9898600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:9894600-9899800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:9894800-9899600	Enhancers	Esophagus	oesophagus
4	chr2:9895200-9898800	Weak transcription	A549	lung
5	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
6	chr2:9895600-9900000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:9895600-9900200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:9895600-9900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:9896200-9901400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:9896800-9898600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr2:9896800-9899600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr2:9896800-9899800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:9897000-9898600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:9897000-9898600	Enhancers	Lung	lung
15	chr2:9897000-9899000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:9897000-9902200	Enhancers	K562	blood
17	chr2:9897200-9898400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:9897200-9898400	Flanking Active TSS	Osteobl	bone
19	chr2:9897200-9898600	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr2:9897200-9899000	Enhancers	HSMM	muscle
21	chr2:9897200-9899200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:9897400-9898400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr2:9897400-9898400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:9897400-9898400	Weak transcription	HMEC	breast
25	chr2:9897400-9898600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr2:9897400-9898600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:9897400-9898600	Enhancers	Fetal Brain Male	brain
28	chr2:9897400-9898600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr2:9897400-9898600	Enhancers	Thymus	Thymus
30	chr2:9897400-9898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:9897400-9899200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:9897600-9898400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:9897600-9898400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:9897600-9898400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:9897600-9898400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:9897600-9898400	Flanking Active TSS	NH-A	brain
37	chr2:9897600-9898600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:9897600-9898600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:9897600-9898600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
40	chr2:9897600-9898600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:9897600-9898800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:9897800-9898400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr2:9897800-9898400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:9897800-9898400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:9897800-9898400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr2:9897800-9898400	Active TSS	Aorta	Aorta
47	chr2:9897800-9898400	Active TSS	Brain Substantia Nigra	brain
48	chr2:9897800-9898400	Active TSS	Colon Smooth Muscle	Colon
49	chr2:9897800-9898400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr2:9897800-9898400	Active TSS	Pancreatic Islets	Pancreatic Islet

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