Variant report

Variant	rs4671990
Chromosome Location	chr2:55129821-55129822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55127373..55130135-chr2:55130954..55133199,2	K562	blood:
2	chr2:55129551..55132200-chr2:55194668..55197954,3	MCF-7	breast:
3	chr2:55129798..55133385-chr2:55275223..55278848,4	MCF-7	breast:
4	chr2:55129480..55132018-chr2:55180693..55183896,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10171653	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12467381	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17046477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304687	0.82[ASN][1000 genomes]
rs34121514	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36126551	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671987	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671988	0.94[EUR][1000 genomes]
rs4671989	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60808665	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6707572	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67299431	0.90[EUR][1000 genomes]
rs919669	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55095200-55148200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55120400-55130200	Weak transcription	Hela-S3	cervix
3	chr2:55122000-55130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:55123400-55130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:55125800-55131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:55126000-55130800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:55126000-55131000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:55126000-55131200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:55126200-55130800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:55127000-55130600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:55127000-55132400	Weak transcription	Fetal Brain Male	brain
12	chr2:55127600-55130400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:55127600-55130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:55127600-55130600	Weak transcription	HSMMtube	muscle
15	chr2:55127600-55131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55127600-55131400	Weak transcription	Fetal Thymus	thymus
17	chr2:55127600-55133400	Weak transcription	Fetal Brain Female	brain
18	chr2:55127800-55130400	Weak transcription	Osteobl	bone
19	chr2:55127800-55133400	Weak transcription	Brain Substantia Nigra	brain
20	chr2:55127800-55133600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:55128000-55130000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:55128000-55130000	Weak transcription	NHEK	skin
23	chr2:55128000-55130800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:55128000-55131000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:55128000-55133400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:55128000-55133400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:55128000-55133800	Weak transcription	Brain Anterior Caudate	brain
28	chr2:55128400-55130800	Weak transcription	Small Intestine	intestine
29	chr2:55129000-55131600	Weak transcription	HepG2	liver
30	chr2:55129200-55130200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:55129200-55130600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:55129200-55130800	Weak transcription	Adipose Nuclei	Adipose
33	chr2:55129200-55130800	Weak transcription	Liver	Liver
34	chr2:55129200-55131000	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:55129200-55131000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:55129200-55131200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:55129200-55133600	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:55129600-55130800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:55129600-55130800	Weak transcription	Fetal Intestine Small	intestine
40	chr2:55129800-55130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:55129800-55130400	Weak transcription	Fetal Intestine Large	intestine
42	chr2:55129800-55130600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:55129800-55131400	Weak transcription	Psoas Muscle	Psoas
44	chr2:55129800-55131400	Enhancers	NHDF-Ad	bronchial

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