Variant report

Variant	rs4687557
Chromosome Location	chr3:52890612-52890613
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	chr3:52888069..52891024-chr3:53081330..53083131,2	K562	blood:
2	chr3:52888488..52890920-chr3:53078565..53080433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10049313	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486028	1.00[EUR][1000 genomes]
rs13066997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991567	1.00[EUR][1000 genomes]
rs2001733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336155	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336157	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.91[AMR][1000 genomes]
rs2336556	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535618	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535638	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535643	0.91[AMR][1000 genomes]
rs2535644	0.91[AMR][1000 genomes]
rs2535645	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[EUR][1000 genomes]
rs2564927	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2710315	1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710318	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710343	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878635	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687676	0.81[AFR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	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	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs7623667	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647534	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
3	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:52879800-52894800	Weak transcription	HSMM	muscle
6	chr3:52880600-52891000	Weak transcription	Fetal Heart	heart
7	chr3:52883400-52894200	Weak transcription	HSMMtube	muscle
8	chr3:52883400-52894600	Weak transcription	Hela-S3	cervix
9	chr3:52883800-52894400	Weak transcription	Psoas Muscle	Psoas
10	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:52884200-52893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:52884400-52893000	Weak transcription	Small Intestine	intestine
14	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52886000-52891000	Strong transcription	Fetal Thymus	thymus
16	chr3:52886200-52907800	Weak transcription	NHLF	lung
17	chr3:52886400-52894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:52886600-52890800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:52886600-52890800	Weak transcription	Pancreas	Pancrea
20	chr3:52886600-52890800	Weak transcription	Right Ventricle	heart
21	chr3:52886600-52891000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:52886600-52891200	Weak transcription	Spleen	Spleen
23	chr3:52886600-52891400	Weak transcription	Brain Substantia Nigra	brain
24	chr3:52886600-52891600	Weak transcription	Fetal Lung	lung
25	chr3:52886600-52894400	Weak transcription	Esophagus	oesophagus
26	chr3:52886600-52894400	Weak transcription	Gastric	stomach
27	chr3:52886600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52886600-52894600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52886600-52895000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:52886600-52899800	Weak transcription	Dnd41	blood
35	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
39	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
41	chr3:52886800-52891800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:52886800-52893600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:52886800-52894400	Weak transcription	Placenta	Placenta
44	chr3:52886800-52894600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:52886800-52894800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:52887000-52890800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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