Variant report

Variant	rs4687690
Chromosome Location	chr3:52953622-52953623
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52947000..52951038-chr3:52951338..52956335,5	K562	blood:
2	chr3:52947000..52950215-chr3:52950921..52954800,3	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10049313	1.00[EUR][1000 genomes]
rs1052728	1.00[EUR][1000 genomes]
rs12486028	1.00[EUR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	1.00[EUR][1000 genomes]
rs1991567	1.00[EUR][1000 genomes]
rs2001733	1.00[EUR][1000 genomes]
rs2001734	1.00[EUR][1000 genomes]
rs2245536	1.00[EUR][1000 genomes]
rs2246888	1.00[EUR][1000 genomes]
rs2246889	1.00[EUR][1000 genomes]
rs2256728	1.00[EUR][1000 genomes]
rs2256734	1.00[EUR][1000 genomes]
rs2276814	1.00[EUR][1000 genomes]
rs2276819	1.00[EUR][1000 genomes]
rs2276821	1.00[EUR][1000 genomes]
rs2336155	1.00[EUR][1000 genomes]
rs2336157	1.00[EUR][1000 genomes]
rs2336158	1.00[EUR][1000 genomes]
rs2336159	1.00[EUR][1000 genomes]
rs2336161	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336556	1.00[EUR][1000 genomes]
rs2336557	1.00[EUR][1000 genomes]
rs2336559	1.00[EUR][1000 genomes]
rs2535615	1.00[EUR][1000 genomes]
rs2535616	1.00[EUR][1000 genomes]
rs2535618	1.00[EUR][1000 genomes]
rs2535619	1.00[EUR][1000 genomes]
rs2535620	1.00[EUR][1000 genomes]
rs2535621	1.00[EUR][1000 genomes]
rs2535622	1.00[EUR][1000 genomes]
rs2535623	1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	1.00[EUR][1000 genomes]
rs2535628	1.00[EUR][1000 genomes]
rs2535631	1.00[EUR][1000 genomes]
rs2535632	1.00[EUR][1000 genomes]
rs2535636	1.00[EUR][1000 genomes]
rs2535637	1.00[EUR][1000 genomes]
rs2535638	1.00[EUR][1000 genomes]
rs2535639	1.00[EUR][1000 genomes]
rs2535641	1.00[EUR][1000 genomes]
rs2535642	1.00[EUR][1000 genomes]
rs2535645	1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[EUR][1000 genomes]
rs2564927	1.00[EUR][1000 genomes]
rs2564943	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2710315	1.00[EUR][1000 genomes]
rs2710316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710318	1.00[EUR][1000 genomes]
rs2710319	1.00[EUR][1000 genomes]
rs2710320	1.00[EUR][1000 genomes]
rs2710321	1.00[EUR][1000 genomes]
rs2710324	1.00[EUR][1000 genomes]
rs2710325	1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	1.00[EUR][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	1.00[EUR][1000 genomes]
rs2710340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710343	1.00[EUR][1000 genomes]
rs2710344	1.00[EUR][1000 genomes]
rs2878633	1.00[EUR][1000 genomes]
rs2878634	1.00[EUR][1000 genomes]
rs2878635	1.00[EUR][1000 genomes]
rs2878636	1.00[EUR][1000 genomes]
rs3774361	1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4234640	1.00[EUR][1000 genomes]
rs4687555	1.00[EUR][1000 genomes]
rs4687557	1.00[EUR][1000 genomes]
rs4687659	1.00[EUR][1000 genomes]
rs4687661	1.00[EUR][1000 genomes]
rs4687665	1.00[EUR][1000 genomes]
rs4687666	1.00[EUR][1000 genomes]
rs4687667	1.00[EUR][1000 genomes]
rs4687668	1.00[EUR][1000 genomes]
rs4687669	1.00[EUR][1000 genomes]
rs4687670	1.00[EUR][1000 genomes]
rs4687671	1.00[EUR][1000 genomes]
rs4687674	1.00[EUR][1000 genomes]
rs4687675	1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687688	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445537	1.00[EUR][1000 genomes]
rs6445540	1.00[EUR][1000 genomes]
rs6445542	1.00[EUR][1000 genomes]
rs6445548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774869	1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs6795138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72961745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72961755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967404	1.00[EUR][1000 genomes]
rs7623667	1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	1.00[EUR][1000 genomes]
rs7637212	1.00[EUR][1000 genomes]
rs7647534	1.00[EUR][1000 genomes]
rs7649515	1.00[EUR][1000 genomes]
rs7650966	1.00[EUR][1000 genomes]
rs7652175	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652476	1.00[EUR][1000 genomes]
rs9681089	1.00[EUR][1000 genomes]
rs9682449	1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9815408	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833487	1.00[EUR][1000 genomes]
rs9846827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869545	1.00[EUR][1000 genomes]
rs9877711	1.00[EUR][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	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
3	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:52932200-52953800	Weak transcription	Ovary	ovary
7	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
8	chr3:52932200-52961800	Weak transcription	A549	lung
9	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
10	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:52932200-52967800	Weak transcription	HSMM	muscle
12	chr3:52932200-52968600	Weak transcription	Osteobl	bone
13	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
15	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
17	chr3:52932400-52968800	Weak transcription	NHEK	skin
18	chr3:52935600-52968600	Strong transcription	Dnd41	blood
19	chr3:52937200-52959800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:52938000-52959000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:52939600-52961200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:52941800-52961600	Weak transcription	Colonic Mucosa	Colon
23	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
24	chr3:52943200-52958800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:52943200-52958800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:52943600-52957000	Strong transcription	Placenta	Placenta
27	chr3:52943600-52962400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:52943600-52964000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:52943800-52956200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52943800-52957600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:52944400-52956400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:52945200-52960000	Weak transcription	Gastric	stomach
33	chr3:52947400-52968000	Weak transcription	Fetal Lung	lung
34	chr3:52947600-52960800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:52947600-52963000	Weak transcription	Fetal Heart	heart
36	chr3:52948200-52955800	Strong transcription	Fetal Intestine Small	intestine
37	chr3:52948800-52955800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52949000-52962400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:52949000-52968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:52949200-52956000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:52949200-52962800	Weak transcription	K562	blood
42	chr3:52950000-52966600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:52951200-52956200	Strong transcription	Adipose Nuclei	Adipose
44	chr3:52951200-52956800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:52951200-52957200	Strong transcription	Primary T cells from cord blood	blood
46	chr3:52951200-52957200	Strong transcription	Fetal Thymus	thymus
47	chr3:52951200-52958800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:52951200-52959000	Strong transcription	Liver	Liver
49	chr3:52951200-52966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:52951400-52954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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