Variant report

Variant	rs6445540
Chromosome Location	chr3:52880024-52880025
allele	A/T
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	chr3:52879780-52880079	GM12892	blood:	n/a	n/a
2	CTCF	chr3:52879808-52880034	K562	blood:	n/a	n/a
3	RAD21	chr3:52879843-52880043	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr3:52879733-52880080	H1-hESC	embryonic stem cell:	n/a	chr3:52879839-52879849
5	CTCF	chr3:52879694-52880094	K562	blood:	n/a	n/a
6	CTCF	chr3:52879798-52880059	K562	blood:	n/a	n/a
7	CTCF	chr3:52879741-52880075	IMR90	lung:	n/a	n/a
8	SMC3	chr3:52879869-52880063	HepG2	liver:	n/a	n/a
9	CTCF	chr3:52879880-52880030	GM06990	blood:	n/a	n/a
10	ZNF143	chr3:52879871-52880071	GM12878	blood:	n/a	n/a
11	CTCF	chr3:52879733-52880085	K562	blood:	n/a	n/a
12	MAZ	chr3:52879875-52880075	K562	blood:	n/a	chr3:52879965-52879975 chr3:52879950-52879960
13	CTCF	chr3:52879808-52880028	GM12878	blood:	n/a	n/a
14	CTCF	chr3:52879880-52880030	GM12873	blood:	n/a	n/a
15	CTCF	chr3:52879782-52880060	GM19238	blood:	n/a	n/a
16	RAD21	chr3:52879648-52880135	H1-hESC	embryonic stem cell:	n/a	chr3:52879839-52879849
17	CTCF	chr3:52879880-52880030	HFF-Myc	foreskin:	n/a	n/a
18	SMC3	chr3:52879734-52880108	GM12878	blood:	n/a	n/a
19	CTCF	chr3:52879880-52880030	HCM	heart:	n/a	n/a
20	CTCF	chr3:52879880-52880030	NHEK	skin:	n/a	n/a
21	MAZ	chr3:52879934-52880110	GM12878	blood:	n/a	chr3:52879965-52879975 chr3:52879950-52879960
22	CTCF	chr3:52879723-52880097	GM12878	blood:	n/a	n/a
23	CTCF	chr3:52879785-52880053	GM19240	blood:	n/a	n/a
24	RAD21	chr3:52879769-52880058	IMR90	lung:	n/a	chr3:52879839-52879849
25	CTCF	chr3:52879690-52880032	H1-hESC	embryonic stem cell:	n/a	n/a
26	SMC3	chr3:52879758-52880045	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr3:52880000-52880150	A549	lung:	n/a	n/a
28	CTCF	chr3:52879880-52880030	GM12875	blood:	n/a	n/a
29	CTCF	chr3:52879785-52880028	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr3:52879900-52880050	RPTEC	kidney:	n/a	n/a
31	CTCF	chr3:52879793-52880025	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:52879816-52880131	HepG2	liver:	n/a	n/a
33	CTCF	chr3:52879739-52880190	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr3:52879722-52880055	SK-N-SH_RA	brain:	n/a	chr3:52879839-52879849
35	RAD21	chr3:52879749-52880088	GM12878	blood:	n/a	chr3:52879839-52879849
36	CTCF	chr3:52879798-52880054	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr3:52879779-52880038	GM12891	blood:	n/a	n/a
38	CTCF	chr3:52879776-52880026	Spleen_OC	spleen:	n/a	n/a
39	CTCF	chr3:52879880-52880030	GM12864	blood:	n/a	n/a
40	CTCF	chr3:52879810-52880030	GM19239	blood:	n/a	n/a
41	CTCF	chr3:52879804-52880031	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:2986443..2986963-chr3:52879382..52880171,2	MCF-7	breast:
2	chr3:52861566..52862446-chr3:52879879..52880402,2	MCF-7	breast:
3	chr3:52873625..52875144-chr3:52879185..52881871,2	K562	blood:
4	chr3:52879907..52880415-chr3:52968439..52969296,2	K562	blood:

Variant related genes	Relation type
TMEM110-MUSTN1	TF binding region
TMEM110	TF binding region
ENSG00000059122	Chromatin interaction
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10049313	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052728	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486028	1.00[EUR][1000 genomes]
rs13066997	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991567	1.00[EUR][1000 genomes]
rs2001733	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336155	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2336556	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535617	0.97[AFR][1000 genomes]
rs2535618	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535643	0.91[AMR][1000 genomes]
rs2535644	0.91[AMR][1000 genomes]
rs2535645	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	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	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.85[AFR][1000 genomes];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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	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	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638431	0.95[AFR][1000 genomes]
rs7645169	0.97[AFR][1000 genomes]
rs7647534	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52866000-52884800	Weak transcription	HMEC	breast
4	chr3:52866200-52885200	Weak transcription	NHEK	skin
5	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
9	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
13	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
14	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52873600-52881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52873600-52882600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:52873600-52889000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:52873800-52882200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:52873800-52889000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:52874200-52883800	Enhancers	Psoas Muscle	Psoas
22	chr3:52874800-52880200	Enhancers	Right Atrium	heart
23	chr3:52875600-52880200	Enhancers	HSMMtube	muscle
24	chr3:52875800-52882600	Weak transcription	NH-A	brain
25	chr3:52875800-52885800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:52876000-52885800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:52876600-52880400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52876600-52881200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:52876800-52880400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:52876800-52881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:52876800-52881600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:52876800-52881600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52876800-52881600	Weak transcription	Dnd41	blood
34	chr3:52876800-52882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:52876800-52883600	Weak transcription	Aorta	Aorta
36	chr3:52877000-52881200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:52877000-52881200	Weak transcription	Ovary	ovary
38	chr3:52877000-52881800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:52877000-52882200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:52877000-52883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52877000-52885000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52877000-52885600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:52877200-52880600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52877200-52881000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:52877200-52882200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:52877400-52881200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:52877400-52881600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:52877800-52881000	Weak transcription	Brain Germinal Matrix	brain
49	chr3:52877800-52881400	Weak transcription	Gastric	stomach
50	chr3:52877800-52881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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