Variant report

Variant	rs59841744
Chromosome Location	chr2:171979335-171979336
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171977326..171979557-chr2:172015386..172018332,2	MCF-7	breast:
2	chr2:171978954..171981322-chr2:171983715..171985729,2	MCF-7	breast:
3	chr2:171978962..171981952-chr2:171996224..171998701,2	K562	blood:
4	chr2:171965727..171968245-chr2:171979215..171980847,2	K562	blood:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10173931	0.92[EUR][1000 genomes]
rs10490606	0.80[AMR][1000 genomes]
rs13389859	1.00[EUR][1000 genomes]
rs16823191	0.85[AMR][1000 genomes]
rs16859087	0.92[EUR][1000 genomes]
rs16859121	0.92[EUR][1000 genomes]
rs16859167	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859176	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859177	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2356600	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2356609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2723245	0.92[EUR][1000 genomes]
rs2723248	0.92[EUR][1000 genomes]
rs2723250	0.90[EUR][1000 genomes]
rs2883940	0.90[EUR][1000 genomes]
rs55644524	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55885449	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55939429	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55995602	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55997598	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56004444	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134465	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56155163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56155601	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56191582	0.90[EUR][1000 genomes]
rs56308745	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56382502	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56934523	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57733560	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58028937	0.81[EUR][1000 genomes]
rs58307585	0.85[AMR][1000 genomes]
rs58685348	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60396936	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60730419	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6711423	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6722196	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736045	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6746133	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6750585	0.90[EUR][1000 genomes]
rs73013435	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73013436	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73013439	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73013453	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73013465	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73017249	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73027220	0.92[EUR][1000 genomes]
rs73029214	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73976125	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73976285	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591214	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9752051	0.82[AMR][1000 genomes];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	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171917000-172000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:171933200-171981000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:171950600-171991200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:171954600-171987200	Weak transcription	Fetal Stomach	stomach
5	chr2:171955800-171980800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:171956400-171980200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:171957200-171980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:171957200-171980000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:171957200-171982400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:171957200-171986000	Weak transcription	Spleen	Spleen
11	chr2:171957200-172010400	Weak transcription	HSMM	muscle
12	chr2:171959600-171980000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:171966600-171981200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:171967000-171980000	Weak transcription	Pancreas	Pancrea
15	chr2:171968400-171981800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:171968800-171985400	Weak transcription	Left Ventricle	heart
17	chr2:171969400-171981000	Weak transcription	NHDF-Ad	bronchial
18	chr2:171971200-171993000	Weak transcription	Gastric	stomach
19	chr2:171971400-171980000	Weak transcription	Ovary	ovary
20	chr2:171971400-171981400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:171973600-171980000	Weak transcription	Liver	Liver
22	chr2:171973600-171981200	Weak transcription	Small Intestine	intestine
23	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:171973800-171979800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:171973800-171989200	Weak transcription	K562	blood
26	chr2:171973800-171990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:171974000-171981200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:171974000-171984400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:171974000-171988600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:171974000-171990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:171974000-171996400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:171974000-172003200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:171974000-172003200	Weak transcription	Fetal Thymus	thymus
34	chr2:171974200-171981200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:171974200-171981400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:171974200-171984800	Weak transcription	GM12878-XiMat	blood
37	chr2:171974200-171985000	Weak transcription	Primary B cells from cord blood	blood
38	chr2:171974200-171993600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:171974200-171996400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:171974200-172002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:171974400-171979400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:171974400-171980400	Weak transcription	HepG2	liver
43	chr2:171974400-171984600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:171974400-171985000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:171974400-171992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:171974400-172003200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:171974600-171984800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:171976000-171980600	Weak transcription	A549	lung
49	chr2:171976000-171981000	Weak transcription	Fetal Lung	lung
50	chr2:171976000-171983400	Weak transcription	Primary B cells from peripheral blood	blood

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