Variant report

Variant	rs55644524
Chromosome Location	chr2:172005210-172005211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172002500..172008778-chr2:172012564..172018500,9	MCF-7	breast:
2	chr2:172004062..172006526-chr2:172009353..172011792,2	MCF-7	breast:
3	chr2:172004769..172008425-chr2:172014877..172017754,3	MCF-7	breast:
4	chr2:171829864..171832222-chr2:172003176..172005661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10173931	0.90[EUR][1000 genomes]
rs10490606	0.86[AFR][1000 genomes]
rs13389859	0.98[EUR][1000 genomes]
rs16823191	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs16859087	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16859121	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16859137	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs16859167	0.98[EUR][1000 genomes]
rs16859176	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16859177	0.86[EUR][1000 genomes]
rs1863679	0.81[AFR][1000 genomes]
rs2356600	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2356609	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723245	0.90[EUR][1000 genomes]
rs2723248	0.90[EUR][1000 genomes]
rs2723250	0.88[EUR][1000 genomes]
rs2883940	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55885449	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55939429	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55995602	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55997598	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56004444	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56134465	0.84[EUR][1000 genomes]
rs56155163	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56155601	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56191582	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56308745	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56382502	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56934523	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57173242	0.89[AFR][1000 genomes]
rs57733560	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58028937	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58307585	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58685348	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59841744	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60396936	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60730419	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61105084	0.81[AMR][1000 genomes]
rs6711423	0.86[EUR][1000 genomes]
rs6722196	0.90[EUR][1000 genomes]
rs6736045	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6746133	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6750585	0.87[EUR][1000 genomes]
rs73013435	0.98[EUR][1000 genomes]
rs73013436	0.98[EUR][1000 genomes]
rs73013439	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73013453	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73013465	0.86[EUR][1000 genomes]
rs73017249	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73017262	0.80[AMR][1000 genomes]
rs73017268	0.81[AMR][1000 genomes]
rs73027220	0.90[EUR][1000 genomes]
rs73027271	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73029214	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73976125	0.86[EUR][1000 genomes]
rs73976285	0.98[EUR][1000 genomes]
rs7591214	0.98[EUR][1000 genomes]
rs7604392	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9752051	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171957200-172010400	Weak transcription	HSMM	muscle
2	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:171985600-172006200	Weak transcription	Esophagus	oesophagus
4	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:171989400-172007000	Weak transcription	Lung	lung
6	chr2:171990000-172016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:171994000-172010400	Weak transcription	Thymus	Thymus
8	chr2:171994200-172010400	Weak transcription	Ovary	ovary
9	chr2:171994800-172005400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:171995400-172012200	Weak transcription	Dnd41	blood
11	chr2:171996600-172006000	Weak transcription	Gastric	stomach
12	chr2:171996600-172015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:171996600-172015400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:171996600-172015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:171997000-172007600	Weak transcription	Placenta	Placenta
16	chr2:171997000-172010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:171998200-172007200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:171998200-172010400	Weak transcription	Psoas Muscle	Psoas
19	chr2:171998400-172014800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:171999000-172014800	Weak transcription	Osteobl	bone
21	chr2:171999200-172014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:171999600-172012200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:171999600-172013800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:171999800-172006000	Weak transcription	Small Intestine	intestine
25	chr2:172000000-172010400	Weak transcription	Spleen	Spleen
26	chr2:172000200-172014600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:172001000-172010800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:172001600-172010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:172001800-172006200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr2:172002000-172007600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:172002200-172005400	Enhancers	Primary B cells from peripheral blood	blood
32	chr2:172002600-172006400	Enhancers	HepG2	liver
33	chr2:172003000-172006000	Weak transcription	Pancreas	Pancrea
34	chr2:172003000-172006200	Weak transcription	Left Ventricle	heart
35	chr2:172003000-172012200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:172003200-172007600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:172003200-172015400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:172003400-172008800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:172003400-172010400	Weak transcription	Fetal Thymus	thymus
40	chr2:172003400-172012200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:172003600-172005600	Weak transcription	Fetal Intestine Small	intestine
42	chr2:172003600-172006000	Weak transcription	Fetal Intestine Large	intestine
43	chr2:172003600-172008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:172003600-172010800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:172003600-172014600	Weak transcription	HMEC	breast
46	chr2:172003800-172010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:172003800-172012400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:172003800-172014600	Weak transcription	NH-A	brain
49	chr2:172004000-172005800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:172004000-172006000	Weak transcription	Stomach Mucosa	stomach

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