Variant report

Variant	rs6445541
Chromosome Location	chr3:52880128-52880129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52880080-52880230	HEEpiC	esophagus:	n/a	n/a
2	CTCF	chr3:52880080-52880230	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr3:52880040-52880190	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:52880080-52880230	HPAF	blood vessel:	n/a	n/a
5	RAD21	chr3:52879648-52880135	H1-hESC	embryonic stem cell:	n/a	chr3:52879839-52879849
6	CTCF	chr3:52880120-52880270	NHEK	skin:	n/a	n/a
7	CTCF	chr3:52880000-52880150	A549	lung:	n/a	n/a
8	CTCF	chr3:52879816-52880131	HepG2	liver:	n/a	n/a
9	CTCF	chr3:52879739-52880190	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr3:52880120-52880270	HPAF	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 79 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10865977	0.89[EUR][1000 genomes]
rs11130331	0.87[CEU][hapmap]
rs11715347	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719137	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11918800	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11922961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11922975	0.92[CEU][hapmap]
rs12487379	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12492391	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs12496077	0.81[ASN][1000 genomes]
rs12638968	0.82[EUR][1000 genomes]
rs13072536	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs13072537	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13083728	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1573815	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2071042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2239547	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2239548	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240915	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240917	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245538	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245647	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2256332	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2276815	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2276817	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2276823	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276825	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2336558	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336664	0.82[EUR][1000 genomes]
rs2336667	0.82[EUR][1000 genomes]
rs2336668	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2535633	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733047	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3774364	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821873	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs4302374	0.82[JPT][hapmap]
rs4350911	0.84[EUR][1000 genomes]
rs4687554	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4687562	0.80[EUR][1000 genomes]
rs4687657	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4687658	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs4687663	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4687672	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4687679	0.81[EUR][1000 genomes]
rs4687680	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4687682	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs4687683	0.82[EUR][1000 genomes]
rs4687687	0.92[CEU][hapmap]
rs56019197	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60332615	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445538	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6445539	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6445547	0.82[JPT][hapmap]
rs6764322	0.84[EUR][1000 genomes]
rs6769789	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773650	0.84[EUR][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6803519	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7612624	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7617468	0.82[ASN][1000 genomes]
rs7620690	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7620706	0.81[ASN][1000 genomes]
rs7626551	0.88[CEU][hapmap]
rs7630552	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638524	0.84[ASN][1000 genomes]
rs7652667	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9682464	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9810807	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs9825230	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9836499	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs9850563	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9860296	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9876403	0.85[JPT][hapmap]
rs9880978	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9985365	0.84[CEU][hapmap]

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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6445541	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs6445541	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6445541	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6445541	ITIH4-AS1	cis	lung	GTEx
rs6445541	ITIH4	cis	multi-tissue	Pritchard
rs6445541	FLJ12442	cis	multi-tissue	Pritchard

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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