Variant report

Variant	rs58080260
Chromosome Location	chr2:128539256-128539257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128537653..128539595-chr2:128543359..128545424,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10171898	1.00[ASN][1000 genomes]
rs10210695	1.00[ASN][1000 genomes]
rs11557685	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674513	1.00[ASN][1000 genomes]
rs11678032	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692524	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11693223	0.85[AFR][1000 genomes]
rs11693759	1.00[ASN][1000 genomes]
rs13397060	0.81[ASN][1000 genomes]
rs13421835	0.81[ASN][1000 genomes]
rs13423029	0.81[ASN][1000 genomes]
rs17418125	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534053	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534123	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599575	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600177	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771291	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56954978	1.00[ASN][1000 genomes]
rs57410763	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57498556	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57913162	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57986825	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59009188	0.86[ASN][1000 genomes]
rs59090605	1.00[ASN][1000 genomes]
rs59727076	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59918187	0.81[ASN][1000 genomes]
rs60087786	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61187878	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61730415	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714620	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734925	1.00[ASN][1000 genomes]
rs6756507	1.00[ASN][1000 genomes]
rs72963794	1.00[ASN][1000 genomes]
rs7560482	0.81[ASN][1000 genomes]
rs7574303	0.81[ASN][1000 genomes]
rs7575961	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585200	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591477	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605158	1.00[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	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv428726	chr2:128387756-128539894	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58080260	WDR33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128479400-128560400	Weak transcription	Esophagus	oesophagus
2	chr2:128498200-128562800	Weak transcription	Pancreas	Pancrea
3	chr2:128507600-128542800	Weak transcription	Stomach Mucosa	stomach
4	chr2:128519200-128543400	Weak transcription	Fetal Stomach	stomach
5	chr2:128522000-128549000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:128522600-128543600	Weak transcription	Gastric	stomach
7	chr2:128522600-128543800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:128522600-128565000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:128522600-128567400	Weak transcription	Aorta	Aorta
10	chr2:128522800-128539400	Weak transcription	HSMMtube	muscle
11	chr2:128522800-128543600	Weak transcription	Lung	lung
12	chr2:128522800-128546000	Weak transcription	Fetal Brain Male	brain
13	chr2:128522800-128564200	Weak transcription	Small Intestine	intestine
14	chr2:128523400-128545200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:128525800-128542800	Weak transcription	Fetal Brain Female	brain
16	chr2:128525800-128545800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:128526000-128540600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:128526000-128553200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:128527600-128563000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:128527800-128564200	Weak transcription	Fetal Lung	lung
21	chr2:128528000-128567000	Weak transcription	Placenta	Placenta
22	chr2:128528200-128554400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:128528600-128543600	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:128528600-128548800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:128528800-128540000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:128528800-128540800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:128528800-128542200	Weak transcription	Primary B cells from cord blood	blood
28	chr2:128528800-128543000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr2:128528800-128554000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:128529000-128541000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:128529000-128543000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:128529000-128543000	Weak transcription	GM12878-XiMat	blood
33	chr2:128529000-128558400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:128529000-128563000	Weak transcription	Hela-S3	cervix
35	chr2:128529200-128543000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:128529200-128543600	Weak transcription	K562	blood
37	chr2:128529200-128548400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:128529200-128553000	Weak transcription	Thymus	Thymus
39	chr2:128529200-128563000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:128529200-128563800	Weak transcription	Fetal Intestine Large	intestine
41	chr2:128529200-128564400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:128529400-128557400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:128529400-128558200	Weak transcription	HSMM	muscle
44	chr2:128529400-128558600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:128529400-128567200	Weak transcription	NHDF-Ad	bronchial
46	chr2:128529600-128540800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:128529600-128564800	Weak transcription	HMEC	breast
48	chr2:128529800-128557600	Weak transcription	NHEK	skin
49	chr2:128530200-128554000	Weak transcription	HUVEC	blood vessel
50	chr2:128530400-128539800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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