Variant report

Variant	rs3749376
Chromosome Location	chr3:24538267-24538268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:247)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:247 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:24538103-24538403	A549	lung:	n/a	n/a
2	CTCF	chr3:24538160-24538310	AoAF	blood vessel:	n/a	n/a
3	CTCFL	chr3:24538095-24538329	K562	blood:	n/a	n/a
4	CTCF	chr3:24538160-24538310	SK-N-SH_RA	brain:	n/a	n/a
5	ZNF143	chr3:24538078-24538407	K562	blood:	n/a	n/a
6	CTCF	chr3:24538200-24538350	K562	blood:	n/a	n/a
7	SMC3	chr3:24537766-24538577	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr3:24538200-24538350	HBMEC	blood vessel:	n/a	n/a
9	CTCF	chr3:24538117-24538389	Medullo	brain:	n/a	n/a
10	CTCF	chr3:24538200-24538350	WERI-Rb-1	eye:	n/a	n/a
11	TAF1	chr3:24538059-24538351	K562	blood:	n/a	n/a
12	CTCF	chr3:24538240-24538390	HFF-Myc	foreskin:	n/a	n/a
13	YY1	chr3:24537987-24538334	HepG2	liver:	n/a	n/a
14	CTCF	chr3:24538200-24538350	AG04450	lung:	n/a	n/a
15	CTCF	chr3:24538160-24538310	HA-sp	spinal cord:	n/a	n/a
16	GTF2F1	chr3:24538114-24538281	K562	blood:	n/a	n/a
17	MAX	chr3:24538086-24538334	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr3:24538184-24538323	GM13977	blood:	n/a	n/a
19	CTCF	chr3:24538200-24538350	A549	lung:	n/a	n/a
20	CTCF	chr3:24538140-24538290	HFF-Myc	foreskin:	n/a	n/a
21	CTCF	chr3:24538043-24538350	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr3:24538180-24538330	HCT-116	colon:	n/a	n/a
23	CTCF	chr3:24538200-24538350	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr3:24538160-24538310	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr3:24538200-24538350	HCPEpiC	choroid plexus:	n/a	n/a
26	CTCF	chr3:24538200-24538350	RPTEC	kidney:	n/a	n/a
27	RCOR1	chr3:24538106-24538310	K562	blood:	n/a	n/a
28	RFX5	chr3:24538046-24538345	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr3:24538180-24538330	GM12865	blood:	n/a	n/a
30	CTCF	chr3:24538180-24538330	GM12874	blood:	n/a	n/a
31	CTCF	chr3:24538149-24538367	Pancreas_OC	pancreas:	n/a	n/a
32	POLR2A	chr3:24537823-24538379	K562	blood:	n/a	n/a
33	RAD21	chr3:24538043-24538364	A549	lung:	n/a	n/a
34	CTCF	chr3:24538160-24538310	HBMEC	blood vessel:	n/a	n/a
35	CTCF	chr3:24538180-24538330	HMF	breast:	n/a	n/a
36	CTCF	chr3:24538140-24538290	HRPEpiC	eye:	n/a	n/a
37	CTCF	chr3:24538021-24538363	HCT-116	colon:	n/a	n/a
38	CTCF	chr3:24538180-24538330	NHLF	lung:	n/a	n/a
39	ZNF384	chr3:24538080-24538431	K562	blood:	n/a	n/a
40	CTCF	chr3:24538180-24538330	HMEC	breast:	n/a	n/a
41	SMC3	chr3:24538004-24538435	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr3:24538200-24538350	AG09319	gingival:	n/a	n/a
43	CTCF	chr3:24538155-24538375	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:24537985-24538362	HCT-116	colon:	n/a	n/a
45	CTCF	chr3:24538160-24538310	HFF	foreskin:	n/a	n/a
46	MYBL2	chr3:24537798-24538362	HepG2	liver:	n/a	n/a
47	CTCF	chr3:24538220-24538370	HCM	heart:	n/a	n/a
48	MBD4	chr3:24538002-24538356	HepG2	liver:	n/a	n/a
49	CTCF	chr3:24538220-24538370	WI-38	lung:	n/a	n/a
50	CTCF	chr3:24538120-24538403	MCF-7	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:24521190..24523090-chr3:24538174..24539755,2	MCF-7	breast:
2	chr3:24400923..24401537-chr3:24537754..24538628,3	MCF-7	breast:
3	chr3:24305947..24306863-chr3:24537889..24538429,2	MCF-7	breast:
4	chr3:24305746..24306763-chr3:24537733..24538685,3	MCF-7	breast:
5	chr3:24536865..24538833-chr6:30851271..30852816,2	MCF-7	breast:
6	chr3:24535191..24540424-chr3:24558354..24564929,10	K562	blood:
7	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
8	chr2:208031298..208032808-chr3:24536314..24538990,2	MCF-7	breast:
9	chr3:24536363..24538620-chr3:25832197..25835181,2	K562	blood:
10	chr3:23988541..23991177-chr3:24537846..24539360,2	K562	blood:
11	chr3:24535945..24538703-chr3:24560979..24563838,8	K562	blood:
12	chr3:24497472..24501858-chr3:24535149..24538807,5	MCF-7	breast:
13	chr3:24534533..24538643-chr3:24561395..24564731,10	MCF-7	breast:
14	chr3:23929854..23930771-chr3:24538163..24538669,2	K562	blood:
15	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1D2-1	chr3:24538155-24538672	ENSG00000228791
2	lnc-NR1D2-1	chr3:24537675-24538309	ENSG00000228791.3
3	lnc-THRB-3	chr3:24537763-24538504	ENSG00000272554.1
4	lnc-NR1D2-1	chr3:24538155-24538309	ENSG00000228791.3

No data

Variant related genes	Relation type
THRB	TF binding region
THRB-AS1	TF binding region
ENSG00000174738	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000265028	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000224822	Chromatin interaction
ENSG00000118263	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13078191	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13090120	0.80[EUR][1000 genomes]
rs1865710	0.94[ASN][1000 genomes]
rs1865711	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs35778241	0.82[EUR][1000 genomes]
rs4858621	0.91[CEU][hapmap]
rs56783261	0.85[ASN][1000 genomes]
rs57751578	0.84[ASN][1000 genomes]
rs58388581	0.89[ASN][1000 genomes]
rs58932894	0.85[ASN][1000 genomes]
rs61063562	0.85[ASN][1000 genomes]
rs6764938	0.89[JPT][hapmap]
rs6765048	0.89[JPT][hapmap]
rs6789815	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs6803476	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6805614	0.82[EUR][1000 genomes]
rs73152119	0.94[ASN][1000 genomes]
rs73823340	0.89[ASN][1000 genomes]
rs73823342	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3341544	chr3:24535373-24538321	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3749376	ZNF343	trans	cerebellum	SCAN
rs3749376	NGLY1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24536600-24538800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:24537200-24538400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr3:24537200-24539600	Weak transcription	HSMMtube	muscle
4	chr3:24537400-24538400	Enhancers	Lung	lung
5	chr3:24537400-24541800	Weak transcription	HSMM	muscle
6	chr3:24537400-24546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:24537600-24538400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:24537600-24538400	Enhancers	HMEC	breast
9	chr3:24537600-24538800	Enhancers	Stomach Mucosa	stomach
10	chr3:24537600-24539600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:24537600-24539600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr3:24537600-24539800	Enhancers	Fetal Intestine Large	intestine
13	chr3:24537600-24542000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:24537800-24538400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:24537800-24538800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:24537800-24539000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr3:24537800-24539000	Enhancers	Duodenum Mucosa	Duodenum
18	chr3:24537800-24539000	Enhancers	A549	lung
19	chr3:24537800-24544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:24538000-24538600	Weak transcription	Pancreas	Pancrea
21	chr3:24538000-24538800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:24538000-24538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:24538000-24540000	Weak transcription	Psoas Muscle	Psoas
24	chr3:24538000-24540200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:24538000-24541600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:24538000-24542000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:24538000-24543600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:24538200-24538400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
29	chr3:24538200-24538400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:24538200-24538600	Active TSS	K562	blood
31	chr3:24538200-24538800	Enhancers	Liver	Liver
32	chr3:24538200-24539000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:24538200-24539000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:24538200-24539000	Enhancers	Hela-S3	cervix
35	chr3:24538200-24539000	Enhancers	HepG2	liver
36	chr3:24538200-24539200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr3:24538200-24539800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:24538200-24539800	Enhancers	Fetal Intestine Small	intestine
39	chr3:24538200-24540200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:24538200-24540200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:24538200-24540400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:24538200-24541200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:24538200-24542200	Weak transcription	NHEK	skin
44	chr3:24538200-24542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:24538200-24547000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:24538200-24552000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:24538200-24560600	Weak transcription	Aorta	Aorta

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