Variant report

Variant	rs2590840
Chromosome Location	chr3:52704032-52704033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52694542..52696482-chr3:52703787..52706365,2	K562	blood:
2	chr3:52541463..52544017-chr3:52702103..52704992,2	MCF-7	breast:
3	chr3:52649013..52651093-chr3:52703505..52705093,2	K562	blood:
4	chr3:52697891..52699504-chr3:52702797..52704715,2	K562	blood:
5	chr3:52703247..52705506-chr3:52723285..52726196,3	K562	blood:

Variant related genes	Relation type
ENSG00000010327	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000238862	Chromatin interaction
ENSG00000222345	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10049313	1.00[EUR][1000 genomes]
rs1052728	1.00[EUR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs17052326	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[YRI][hapmap];0.92[AFR][1000 genomes];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[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[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]
rs2577828	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2577838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590841	0.90[AFR][1000 genomes];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]
rs2710328	1.00[EUR][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	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]
rs34296002	1.00[AMR][1000 genomes]
rs3774361	1.00[EUR][1000 genomes]
rs4234635	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	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]
rs56866386	1.00[EUR][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]
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]
rs72947525	1.00[EUR][1000 genomes]
rs72947530	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72947531	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72947532	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72947537	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72947557	1.00[EUR][1000 genomes]
rs72959348	1.00[EUR][1000 genomes]
rs72965274	1.00[EUR][1000 genomes]
rs7614424	1.00[YRI][hapmap]
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]
rs9682449	1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9877711	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

No data

Chromatin state (count:126 , 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	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:52637200-52715800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52642600-52711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:52650000-52712200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:52655200-52716400	Strong transcription	Fetal Thymus	thymus
7	chr3:52656600-52704600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:52660800-52704800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:52670400-52704600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:52670800-52715400	Strong transcription	Dnd41	blood
12	chr3:52681200-52716200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:52684800-52709000	Weak transcription	Stomach Mucosa	stomach
14	chr3:52688000-52714800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52689000-52704600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52690200-52704600	Weak transcription	Fetal Heart	heart
17	chr3:52693800-52709400	Weak transcription	Right Ventricle	heart
18	chr3:52695200-52705800	Weak transcription	Pancreas	Pancrea
19	chr3:52696000-52712000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:52696200-52704400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:52696200-52704400	Weak transcription	A549	lung
22	chr3:52696200-52705800	Weak transcription	Colonic Mucosa	Colon
23	chr3:52696200-52706000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:52696200-52711800	Weak transcription	Aorta	Aorta
25	chr3:52696400-52704600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:52696400-52710200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:52697400-52704600	Weak transcription	K562	blood
28	chr3:52697600-52704600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:52697600-52704800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:52697600-52705000	Weak transcription	Fetal Kidney	kidney
31	chr3:52697600-52706000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:52697600-52710200	Weak transcription	Fetal Brain Male	brain
33	chr3:52697800-52704600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:52698200-52706000	Weak transcription	Esophagus	oesophagus
35	chr3:52698800-52714400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:52699000-52704400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:52699200-52704600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:52699200-52707200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:52699400-52706400	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:52699400-52707000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:52699400-52715600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:52699800-52704400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:52699800-52704600	Weak transcription	Left Ventricle	heart
44	chr3:52699800-52708400	Weak transcription	Psoas Muscle	Psoas
45	chr3:52700000-52706200	Strong transcription	HepG2	liver
46	chr3:52700000-52710800	Weak transcription	Small Intestine	intestine
47	chr3:52700600-52704600	Weak transcription	Spleen	Spleen
48	chr3:52700600-52715000	Strong transcription	Primary B cells from cord blood	blood
49	chr3:52700800-52704200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:52701200-52704600	Weak transcription	Brain Angular Gyrus	brain

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