Variant report

Variant	rs1546120
Chromosome Location	chr4:120984077-120984078
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	POLR2A	chr4:120984033-120984137	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:120983169-120986309	K562	blood:	n/a	n/a
3	FOS	chr4:120984047-120984159	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:120984048-120984313	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr4:120984022-120984159	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr4:120984018-120984128	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120965543..120968090-chr4:120982539..120985159,2	K562	blood:
2	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:

Variant related genes	Relation type
MAD2L1	TF binding region
ENSG00000250938	TF binding region
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13112411	0.91[CEU][hapmap]
rs13121806	0.81[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs13128669	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1362595	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs1972014	0.88[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2111143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538838	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2908986	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2908988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2908989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908990	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2934379	0.88[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3113988	0.84[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs6817243	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7661491	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv879851	chr4:120942372-120984077	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1546120	QRFPR	cis	parietal	SCAN
rs1546120	BBS12	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120962200-120987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:120971000-120987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120971200-120985200	Weak transcription	Fetal Kidney	kidney
4	chr4:120971200-120985600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:120971200-120986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:120971200-120986400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:120971200-120986800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:120971200-120987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:120971200-120987200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:120971200-120987400	Weak transcription	Left Ventricle	heart
11	chr4:120974800-120985200	Weak transcription	NHEK	skin
12	chr4:120975000-120985400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:120975000-120985400	Weak transcription	Fetal Stomach	stomach
14	chr4:120975000-120985600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:120975400-120984200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:120975400-120986800	Weak transcription	Primary B cells from cord blood	blood
17	chr4:120975600-120984800	Strong transcription	Fetal Thymus	thymus
18	chr4:120975800-120985400	Weak transcription	Primary T cells from cord blood	blood
19	chr4:120975800-120986800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:120976200-120985200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:120976200-120985200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:120976200-120985600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:120976400-120984400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:120976400-120985400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:120977400-120985400	Weak transcription	Fetal Lung	lung
26	chr4:120977400-120986600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:120977400-120986600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:120977400-120986800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:120977400-120987200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:120978000-120985200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:120978000-120985400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:120978200-120984200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:120978200-120987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:120978400-120984200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:120978400-120986600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:120978600-120984400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:120979400-120984200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:120979400-120985400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:120979600-120985200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:120979600-120986800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:120979800-120984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:120979800-120985000	Weak transcription	Thymus	Thymus
43	chr4:120980000-120984400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:120980000-120985000	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:120980200-120984600	Weak transcription	Fetal Intestine Large	intestine
46	chr4:120980200-120985000	Weak transcription	Fetal Intestine Small	intestine
47	chr4:120980200-120985600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:120980400-120984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:120980600-120984600	Strong transcription	HSMM	muscle
50	chr4:120981200-120984600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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