Variant report

Variant	rs3861570
Chromosome Location	chr2:54044560-54044561
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	chr2:54039340..54040877-chr2:54043663..54046202,2	K562	blood:
2	chr2:54043746..54045589-chr2:54047381..54048993,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10181752	0.84[ASN][1000 genomes]
rs10181876	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10187718	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10190578	0.81[ASN][1000 genomes]
rs10191950	0.82[ASN][1000 genomes]
rs10193711	0.92[ASN][1000 genomes]
rs10197062	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10200897	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10211188	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10211650	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10490470	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12162343	0.83[EUR][1000 genomes]
rs12612589	0.84[ASN][1000 genomes]
rs12616124	0.82[ASN][1000 genomes]
rs12616774	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12617668	0.83[ASN][1000 genomes]
rs12618587	0.88[ASN][1000 genomes]
rs12620190	0.87[ASN][1000 genomes]
rs12620208	0.87[ASN][1000 genomes]
rs12620325	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13383167	0.90[ASN][1000 genomes]
rs13393197	0.94[ASN][1000 genomes]
rs13414183	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13414472	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13423576	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17045215	0.87[ASN][1000 genomes]
rs17045292	0.85[ASN][1000 genomes]
rs2272249	0.80[ASN][1000 genomes]
rs2272250	0.83[ASN][1000 genomes]
rs2287344	0.87[ASN][1000 genomes]
rs2287345	0.87[ASN][1000 genomes]
rs28439002	0.92[ASN][1000 genomes]
rs3770398	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3770400	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3821080	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3850345	0.84[ASN][1000 genomes]
rs55839073	0.94[ASN][1000 genomes]
rs6705484	0.87[ASN][1000 genomes]
rs6712204	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6714424	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6717642	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72799229	0.83[ASN][1000 genomes]
rs72799234	0.83[ASN][1000 genomes]
rs72799236	0.80[ASN][1000 genomes]
rs7568771	0.94[ASN][1000 genomes]
rs7582542	0.84[ASN][1000 genomes]
rs7586686	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7609067	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
3	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
4	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
8	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:54020600-54048600	Strong transcription	Osteobl	bone
11	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
16	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
19	chr2:54021600-54046400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:54022000-54044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr2:54022000-54047000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:54022000-54047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54022200-54046200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:54022200-54046600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:54022200-54047200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:54024800-54045400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
32	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:54027200-54046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:54028400-54044600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54030200-54047200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
37	chr2:54031400-54047200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:54031800-54045600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:54032800-54046800	Strong transcription	Primary B cells from cord blood	blood
40	chr2:54033000-54047200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:54033400-54045400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:54033600-54044600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:54034400-54047200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:54034600-54047200	Strong transcription	HSMM	muscle
45	chr2:54035200-54046200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
47	chr2:54037000-54046400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:54037200-54046000	Strong transcription	NH-A	brain
49	chr2:54037200-54046200	Weak transcription	Pancreas	Pancrea
50	chr2:54037200-54047200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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