Variant report

Variant	rs2577829
Chromosome Location	chr3:52658653-52658654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10049313	1.00[EUR][1000 genomes]
rs1052728	1.00[EUR][1000 genomes]
rs17052326	1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	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[TSI][hapmap];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]
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[TSI][hapmap];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[TSI][hapmap];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]
rs2577828	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2590841	1.00[EUR][1000 genomes]
rs2590849	0.81[AFR][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[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710325	1.00[EUR][1000 genomes]
rs2710328	1.00[EUR][1000 genomes]
rs2710329	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710336	1.00[TSI][hapmap];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]
rs4234635	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4234636	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4687555	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]
rs56866386	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6445537	1.00[EUR][1000 genomes]
rs6445540	1.00[EUR][1000 genomes]
rs6445542	1.00[EUR][1000 genomes]
rs6766038	1.00[EUR][1000 genomes]
rs6774869	1.00[EUR][1000 genomes]
rs6776990	1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs72947525	1.00[EUR][1000 genomes]
rs72947530	1.00[EUR][1000 genomes]
rs72947531	1.00[EUR][1000 genomes]
rs72947532	1.00[EUR][1000 genomes]
rs72947537	1.00[EUR][1000 genomes]
rs72947557	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72959348	1.00[EUR][1000 genomes]
rs72965274	1.00[EUR][1000 genomes]
rs7623667	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]
rs7652476	1.00[EUR][1000 genomes]
rs9681089	1.00[EUR][1000 genomes]
rs9682819	1.00[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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2577829	PFN2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52634800-52686000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr3:52636000-52703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52636000-52704000	Strong transcription	Placenta	Placenta
7	chr3:52636200-52703200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:52636600-52669200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:52636600-52673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52636600-52677400	Weak transcription	Pancreas	Pancrea
11	chr3:52636800-52662800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:52636800-52703600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52639600-52670000	Strong transcription	Dnd41	blood
15	chr3:52640600-52663200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:52640800-52684600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:52641000-52670800	Weak transcription	Stomach Mucosa	stomach
18	chr3:52641600-52664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52642400-52671000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:52642400-52676400	Weak transcription	Small Intestine	intestine
21	chr3:52642600-52711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:52643400-52658800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:52643400-52691200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:52643600-52677200	Weak transcription	Fetal Heart	heart
25	chr3:52643800-52660200	Weak transcription	Fetal Brain Male	brain
26	chr3:52643800-52682800	Weak transcription	K562	blood
27	chr3:52648400-52660400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:52649400-52668800	Strong transcription	Primary B cells from cord blood	blood
29	chr3:52649800-52669800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:52650400-52660200	Weak transcription	Hela-S3	cervix
32	chr3:52650800-52661400	Weak transcription	Right Ventricle	heart
33	chr3:52651400-52662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52651400-52666400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:52651600-52658800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:52651800-52659600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:52652400-52660000	Strong transcription	Fetal Stomach	stomach
38	chr3:52652800-52672400	Weak transcription	Gastric	stomach
39	chr3:52652800-52673600	Weak transcription	Aorta	Aorta
40	chr3:52653000-52671400	Weak transcription	Spleen	Spleen
41	chr3:52654000-52667600	Weak transcription	Colonic Mucosa	Colon
42	chr3:52654000-52669600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:52654600-52658800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:52654600-52659600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:52654800-52659800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:52654800-52660200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:52655000-52658800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:52655200-52660000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
50	chr3:52655400-52669200	Strong transcription	HSMM	muscle

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