Variant report

Variant	rs4687621
Chromosome Location	chr3:52524974-52524975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52524920-52525070	HCPEpiC	choroid plexus:	n/a	n/a
2	FOS	chr3:52524711-52525340	HUVEC	blood vessel:	n/a	chr3:52525112-52525123 chr3:52525114-52525122
3	POLR2A	chr3:52524786-52525478	HUVEC	blood vessel:	n/a	n/a
4	MYC	chr3:52524765-52525498	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:52524883-52525195	K562	blood:	n/a	n/a
6	POLR2A	chr3:52524510-52525509	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:52524793-52525393	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:52524760-52525395	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr3:52524842-52525404	HUVEC	blood vessel:	n/a	n/a
10	EGR1	chr3:52524753-52525016	K562	blood:	n/a	chr3:52524920-52524930
11	GATA2	chr3:52524525-52525446	HUVEC	blood vessel:	n/a	chr3:52525235-52525245 chr3:52524944-52524961
12	POLR2A	chr3:52524570-52525506	HUVEC	blood vessel:	n/a	n/a
13	JUN	chr3:52524928-52525324	HUVEC	blood vessel:	n/a	chr3:52525114-52525122
14	POLR2A	chr3:52524935-52525197	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:52524938-52525214	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52514786..52517540-chr3:52524026..52525964,2	K562	blood:
2	chr3:52523610..52525398-chr3:52527726..52530497,3	K562	blood:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011064	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035003	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865972	0.91[EUR][1000 genomes]
rs11721286	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	0.83[EUR][1000 genomes]
rs123603	0.83[EUR][1000 genomes]
rs13074649	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	0.91[EUR][1000 genomes]
rs2109557	0.88[EUR][1000 genomes]
rs2109558	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2215466	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335928	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	0.88[EUR][1000 genomes]
rs3755810	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409803	0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419604	0.88[EUR][1000 genomes]
rs419752	0.83[EUR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	0.85[EUR][1000 genomes]
rs575476	0.88[EUR][1000 genomes]
rs613519	0.81[EUR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445483	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771558	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787493	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.81[EUR][1000 genomes]
rs6810027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887514	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs929528	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	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
7	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 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	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
8	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
10	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:52504200-52527600	Strong transcription	Dnd41	blood
15	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
19	chr3:52504400-52527400	Strong transcription	Osteobl	bone
20	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
23	chr3:52504800-52527400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:52504800-52528000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:52505000-52527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:52506400-52527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:52507400-52527800	Strong transcription	Fetal Thymus	thymus
28	chr3:52508000-52532200	Weak transcription	K562	blood
29	chr3:52509400-52528000	Strong transcription	Gastric	stomach
30	chr3:52509600-52528200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:52510000-52526400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:52510200-52526200	Strong transcription	Pancreas	Pancrea
33	chr3:52510600-52528600	Weak transcription	Fetal Brain Male	brain
34	chr3:52511400-52528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:52513400-52541400	Weak transcription	A549	lung
36	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
37	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
38	chr3:52515600-52528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:52516200-52526000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:52517200-52528200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:52518000-52526800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52518600-52527200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:52518600-52527400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:52518600-52527400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:52518800-52525400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:52518800-52527000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:52518800-52527000	Strong transcription	HSMMtube	muscle
48	chr3:52518800-52527200	Strong transcription	NHEK	skin
49	chr3:52518800-52527600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:52518800-52527800	Strong transcription	Placenta Amnion	Placenta Amnion

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