Variant report

Variant	rs883537
Chromosome Location	chr3:120462324-120462325
allele	C/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	MAX	chr3:120460700-120462875	Hela-S3	cervix:	n/a	chr3:120462809-120462818 chr3:120461753-120461762
2	POLR2A	chr3:120460819-120462715	HUVEC	blood vessel:	n/a	n/a
3	SMC3	chr3:120462133-120462324	K562	blood:	n/a	n/a
4	POLR2A	chr3:120460632-120462709	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr3:120460556-120462518	GM12878	blood:	n/a	chr3:120461055-120461070
6	MAX	chr3:120460478-120463014	A549	lung:	n/a	chr3:120462809-120462818 chr3:120461753-120461762
7	POLR2A	chr3:120460180-120462970	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:120462282-120462901	ProgFib	skin:	n/a	n/a
9	POLR2A	chr3:120460599-120462687	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:120460738-120464825	K562	blood:	n/a	n/a
11	POLR2A	chr3:120460650-120462938	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:120460605-120462512	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:120459890-120462466	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:120461016-120462543	GM12878	blood:	n/a	n/a
15	WRNIP1	chr3:120462316-120462849	GM12878	blood:	n/a	n/a
16	HCFC1	chr3:120460628-120463028	Hela-S3	cervix:	n/a	n/a
17	MAX	chr3:120460610-120462937	K562	blood:	n/a	chr3:120462809-120462818 chr3:120461753-120461762
18	MXI1	chr3:120459474-120463327	SK-N-SH	brain:	n/a	chr3:120461055-120461070 chr3:120462768-120462777
19	POLR2A	chr3:120460664-120462893	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:120460688-120462566	PBDE	blood:	n/a	n/a
21	MAX	chr3:120460618-120462843	MCF-7	breast:	n/a	chr3:120462809-120462818 chr3:120461753-120461762
22	POLR2A	chr3:120460579-120462510	HL-60	blood:	n/a	n/a
23	MYC	chr3:120461979-120462865	MCF10A-Er-Src	breast:	n/a	chr3:120462809-120462818
24	MAX	chr3:120460683-120462618	Hela-S3	cervix:	n/a	chr3:120461753-120461762
25	POLR2A	chr3:120460685-120462958	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:120460327-120462605	MCF10A-Er-Src	breast:	n/a	n/a
27	CHD1	chr3:120461843-120462579	H1-hESC	embryonic stem cell:	n/a	n/a
28	GTF2F1	chr3:120460329-120462831	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:120460675-120462876	Hela-S3	cervix:	n/a	n/a
30	MAX	chr3:120460415-120462342	GM12878	blood:	n/a	chr3:120461753-120461762
31	YY1	chr3:120462210-120462344	K562	blood:	n/a	chr3:120462292-120462300
32	POLR2A	chr3:120460005-120463213	GM12891	blood:	n/a	n/a
33	MAX	chr3:120460677-120462374	SK-N-SH	brain:	n/a	chr3:120461753-120461762
34	POLR2A	chr3:120461052-120462491	HUVEC	blood vessel:	n/a	n/a
35	MYC	chr3:120460666-120462670	NB4	blood:	n/a	chr3:120461753-120461762
36	POLR2A	chr3:120462236-120462391	HUVEC	blood vessel:	n/a	n/a
37	SMC3	chr3:120460733-120462552	Hela-S3	cervix:	n/a	n/a
38	MAX	chr3:120460244-120462774	NB4	blood:	n/a	chr3:120461753-120461762
39	POLR2A	chr3:120460522-120462460	U87	brain:	n/a	n/a
40	UBTF	chr3:120462308-120462372	K562	blood:	n/a	n/a
41	POLR2A	chr3:120461028-120462818	H1-hESC	embryonic stem cell:	n/a	n/a
42	BHLHE40	chr3:120462293-120462511	K562	blood:	n/a	n/a
43	MXI1	chr3:120461409-120462331	K562	blood:	n/a	n/a
44	POLR2A	chr3:120460148-120462949	SK-N-MC	brain:	n/a	n/a
45	MYC	chr3:120460720-120462814	K562	blood:	n/a	chr3:120461753-120461762
46	MYC	chr3:120462313-120462678	MCF10A-Er-Src	breast:	n/a	n/a
47	MTA3	chr3:120460566-120462438	GM12878	blood:	n/a	n/a
48	MYC	chr3:120460707-120462866	Hela-S3	cervix:	n/a	chr3:120462809-120462818 chr3:120461753-120461762
49	SIN3A	chr3:120460700-120462769	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chr3:120460250-120462876	K562	blood:	n/a	chr3:120462809-120462818 chr3:120461753-120461762

No.	Distal block	Cell Line	Cell type
1	chr3:120313507..120317684-chr3:120458763..120463692,6	MCF-7	breast:
2	chr3:120461569..120462386-chr9:140135123..140135683,2	Hela-S3	cervix:
3	chr3:120319088..120321707-chr3:120460414..120462784,2	MCF-7	breast:
4	chr19:12900745..12903543-chr3:120461403..120464027,2	MCF-7	breast:
5	chr3:120315040..120318401-chr3:120459431..120463263,5	MCF-7	breast:
6	chr3:120457859..120461231-chr3:120462100..120464512,3	K562	blood:

Variant related genes	Relation type
RABL3	TF binding region
ENSG00000095066	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000065518	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16831690	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17240621	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378561	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378759	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs424413	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4676823	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537922	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795615	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61796373	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61796376	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624496	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6772101	0.85[AFR][1000 genomes]
rs6785511	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612975	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836215	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120459800-120462600	Active TSS	A549	lung
2	chr3:120460000-120462600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:120460200-120462400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr3:120460200-120462400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:120460200-120462400	Active TSS	Psoas Muscle	Psoas
6	chr3:120460200-120462400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr3:120460200-120462600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:120460200-120462800	Active TSS	Fetal Brain Female	brain
9	chr3:120460200-120463000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:120460200-120463000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:120460200-120463200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:120460200-120463400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:120460400-120462400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:120460400-120462400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:120460400-120462400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:120460400-120462400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:120460400-120462400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:120460400-120462400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:120460400-120462400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:120460400-120462400	Active TSS	Fetal Intestine Large	intestine
21	chr3:120460400-120462400	Active TSS	NHLF	lung
22	chr3:120460400-120462600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:120460400-120462800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:120460400-120463000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:120460400-120463200	Active TSS	GM12878-XiMat	blood
26	chr3:120460600-120462400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:120460600-120462400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:120460600-120462400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:120460600-120462400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:120460600-120462400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:120460600-120462400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:120460600-120462400	Active TSS	Esophagus	oesophagus
33	chr3:120460600-120462400	Active TSS	Fetal Intestine Small	intestine
34	chr3:120460600-120462400	Active TSS	Fetal Stomach	stomach
35	chr3:120460600-120462400	Active TSS	Ovary	ovary
36	chr3:120460600-120462400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr3:120460600-120462400	Active TSS	Right Atrium	heart
38	chr3:120460600-120462400	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr3:120460600-120462400	Bivalent/Poised TSS	HepG2	liver
40	chr3:120460600-120462400	Active TSS	HSMM	muscle
41	chr3:120460600-120462400	Active TSS	HSMMtube	muscle
42	chr3:120460600-120462600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr3:120460600-120462600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:120460600-120462600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:120460600-120462600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:120460600-120462600	Active TSS	Fetal Muscle Trunk	muscle
47	chr3:120460600-120462600	Active TSS	Gastric	stomach
48	chr3:120460600-120462600	Active TSS	Pancreas	Pancrea
49	chr3:120460600-120463200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:120460800-120462400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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