Variant report

Variant	rs34827613
Chromosome Location	chr3:52419291-52419292
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:131)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:131 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52419280-52419430	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr3:52419235-52419553	GM19239	blood:	n/a	n/a
3	TCF12	chr3:52419168-52419479	H1-hESC	embryonic stem cell:	n/a	chr3:52419287-52419297
4	CTCF	chr3:52419064-52419669	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:52419271-52419518	GM20000	blood:	n/a	n/a
6	CTCF	chr3:52419023-52419581	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:52419130-52419656	H1-hESC	embryonic stem cell:	n/a	n/a
8	SMC3	chr3:52419169-52419561	K562	blood:	n/a	n/a
9	RAD21	chr3:52419232-52419562	GM12878	blood:	n/a	n/a
10	TCF12	chr3:52419174-52419433	H1-hESC	embryonic stem cell:	n/a	chr3:52419287-52419297
11	RAD21	chr3:52419068-52419608	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:52418761-52420060	HCT-116	colon:	n/a	n/a
13	ELF1	chr3:52419128-52419523	K562	blood:	n/a	n/a
14	CTCF	chr3:52419260-52419529	LNCaP	prostate:	n/a	n/a
15	RAD21	chr3:52419215-52419611	ECC-1	luminal epithelium:	n/a	n/a
16	YY1	chr3:52419255-52419573	K562	blood:	n/a	n/a
17	CTCF	chr3:52419136-52419775	A549	lung:	n/a	n/a
18	CTCF	chr3:52419257-52419549	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr3:52419186-52419498	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:52419249-52419512	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr3:52419239-52419552	MCF-7	breast:	n/a	n/a
22	SIN3A	chr3:52419210-52419574	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr3:52419203-52419542	T-47D	breast:	n/a	n/a
24	MYC	chr3:52419268-52419486	K562	blood:	n/a	n/a
25	CTCF	chr3:52419244-52419458	A549	lung:	n/a	n/a
26	CTCF	chr3:52419271-52419554	GM19240	blood:	n/a	n/a
27	MAX	chr3:52418861-52419613	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr3:52419221-52419483	K562	blood:	n/a	n/a
29	YY1	chr3:52419249-52419487	HCT-116	colon:	n/a	n/a
30	RAD21	chr3:52419204-52419564	HepG2	liver:	n/a	n/a
31	CTCF	chr3:52419200-52419552	HepG2	liver:	n/a	n/a
32	CTCF	chr3:52419167-52419616	GM12878	blood:	n/a	n/a
33	ATF2	chr3:52419081-52419540	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr3:52419099-52419609	A549	lung:	n/a	n/a
35	ZNF143	chr3:52419202-52419595	K562	blood:	n/a	chr3:52419219-52419237
36	MYC	chr3:52419227-52419523	K562	blood:	n/a	n/a
37	CBX3	chr3:52419214-52419450	K562	blood:	n/a	n/a
38	CTCF	chr3:52419280-52419519	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr3:52419223-52419566	MCF-7	breast:	n/a	n/a
40	NFYA	chr3:52419280-52419531	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr3:52419262-52419498	HepG2	liver:	n/a	n/a
42	MAX	chr3:52418924-52419638	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr3:52419209-52419699	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr3:52419247-52419511	A549	lung:	n/a	n/a
45	CTCF	chr3:52419249-52419543	GM19238	blood:	n/a	n/a
46	CTCF	chr3:52419069-52419747	MCF-7	breast:	n/a	n/a
47	RAD21	chr3:52419096-52419656	MCF-7	breast:	n/a	n/a
48	CTCF	chr3:52419229-52419563	GM12878	blood:	n/a	n/a
49	TEAD4	chr3:52419207-52419550	K562	blood:	n/a	n/a
50	RAD21	chr3:52419240-52419567	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52390322..52390942-chr3:52419226..52419756,2	MCF-7	breast:
2	chr3:52265330..52266149-chr3:52419100..52419914,3	MCF-7	breast:
3	chr3:52409617..52410373-chr3:52418918..52419802,2	MCF-7	breast:
4	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
5	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:
6	chr3:52417646..52419633-chr3:52427141..52429789,2	K562	blood:
7	chr3:52280316..52283002-chr3:52418190..52421140,2	K562	blood:
8	chr3:52035497..52036188-chr3:52418905..52419682,3	MCF-7	breast:
9	chr3:52325194..52326110-chr3:52418963..52419968,4	K562	blood:
10	chr3:52419090..52421222-chr3:52428572..52431039,2	MCF-7	breast:
11	chr3:52325390..52326371-chr3:52418909..52419771,3	MCF-7	breast:
12	chr3:52325192..52326082-chr3:52419115..52419793,5	MCF-7	breast:
13	chr3:52265291..52266190-chr3:52418948..52419840,4	K562	blood:

No data

Variant related genes	Relation type
DNAH1	TF binding region
ENSG00000164088	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000239557	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1011062	0.82[AMR][1000 genomes]
rs1011064	0.82[AMR][1000 genomes]
rs1035002	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1035003	0.82[AMR][1000 genomes]
rs11706001	0.87[ASN][1000 genomes]
rs11707864	1.00[ASN][1000 genomes]
rs11707931	1.00[ASN][1000 genomes]
rs11709658	1.00[ASN][1000 genomes]
rs11716017	1.00[ASN][1000 genomes]
rs123598	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123603	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060192	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065677	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13071708	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13074649	0.91[AMR][1000 genomes]
rs13075370	1.00[ASN][1000 genomes]
rs13076508	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089892	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091360	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093555	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098856	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs164636	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs164637	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17052068	1.00[ASN][1000 genomes]
rs2109557	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215466	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2335640	1.00[ASN][1000 genomes]
rs2335928	0.82[AMR][1000 genomes]
rs2335929	0.82[AMR][1000 genomes]
rs2878549	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332947	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355561	1.00[ASN][1000 genomes]
rs34385735	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34551211	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34628357	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	1.00[ASN][1000 genomes]
rs34908451	1.00[ASN][1000 genomes]
rs35130772	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35133416	1.00[ASN][1000 genomes]
rs352141	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs352144	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs353545	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353548	0.88[EUR][1000 genomes]
rs35982798	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752819	1.00[ASN][1000 genomes]
rs3755810	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3774409	0.91[AMR][1000 genomes]
rs3796342	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs409803	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419604	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419752	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312651	0.82[AMR][1000 genomes]
rs4687541	0.91[AMR][1000 genomes]
rs4687614	0.84[AMR][1000 genomes]
rs498778	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357549	1.00[ASN][1000 genomes]
rs575476	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[ASN][1000 genomes]
rs613519	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61734640	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414568	0.82[AMR][1000 genomes]
rs6445484	0.82[AMR][1000 genomes]
rs6445485	0.82[AMR][1000 genomes]
rs6445486	0.82[AMR][1000 genomes]
rs67248391	1.00[ASN][1000 genomes]
rs676034	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6763882	0.87[ASN][1000 genomes]
rs6771558	0.91[AMR][1000 genomes]
rs6782162	0.82[AMR][1000 genomes]
rs67834575	1.00[ASN][1000 genomes]
rs6794675	1.00[ASN][1000 genomes]
rs6795333	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297391	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297394	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297395	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929528	0.82[AMR][1000 genomes]
rs929529	0.82[AMR][1000 genomes]
rs9847332	0.82[AMR][1000 genomes]
rs9850471	0.91[AMR][1000 genomes]
rs9855470	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	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
5	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3418861	chr3:52415012-52419710	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
3	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
5	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
6	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
8	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
10	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:52407600-52420800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
18	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:52409800-52425200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:52410000-52425200	Weak transcription	Primary B cells from cord blood	blood
21	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:52410200-52420400	Weak transcription	Colonic Mucosa	Colon
24	chr3:52410200-52425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:52410200-52426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:52410400-52419400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:52410400-52420400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:52410600-52420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:52410600-52420200	Weak transcription	Fetal Intestine Large	intestine
30	chr3:52410600-52422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:52410600-52424800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:52410600-52425000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:52411000-52419400	Weak transcription	Primary T cells from cord blood	blood
35	chr3:52411000-52420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:52411000-52420800	Weak transcription	Lung	lung
37	chr3:52411000-52425200	Weak transcription	Pancreas	Pancrea
38	chr3:52411200-52420000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:52411400-52422200	Weak transcription	Placenta	Placenta
40	chr3:52411400-52424800	Weak transcription	Gastric	stomach
41	chr3:52412800-52420400	Weak transcription	Thymus	Thymus
42	chr3:52413800-52420800	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:52413800-52433000	Weak transcription	Fetal Brain Female	brain
44	chr3:52414000-52433200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
46	chr3:52414200-52421400	Weak transcription	Brain Substantia Nigra	brain
47	chr3:52414200-52425000	Weak transcription	Right Ventricle	heart
48	chr3:52414600-52421000	Weak transcription	Ovary	ovary
49	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:52416600-52425200	Weak transcription	Esophagus	oesophagus

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