Variant report

Variant	rs2934379
Chromosome Location	chr4:120986142-120986143
allele	A/G
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	chr4:120983169-120986309	K562	blood:	n/a	n/a
2	E2F4	chr4:120985855-120988544	MCF10A-Er-Src	breast:	n/a	chr4:120987957-120987968 chr4:120988011-120988020

No.	Distal block	Cell Line	Cell type
1	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:
2	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
3	chr4:120973859..120975620-chr4:120985435..120987169,2	K562	blood:
4	chr4:120230931..120233394-chr4:120986011..120987625,2	K562	blood:
5	chr4:120153288..120155840-chr4:120986022..120987789,2	K562	blood:
6	chr4:120985605..120987258-chr4:121004705..121006717,2	K562	blood:

Variant related genes	Relation type
MAD2L1	TF binding region
ENSG00000250938	TF binding region
ENSG00000145390	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11727480	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs12711084	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs13112411	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13121806	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136371	0.84[ASN][1000 genomes]
rs1546120	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]
rs1972014	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]
rs2111143	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28538838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892890	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs2904883	0.88[ASN][1000 genomes]
rs2904884	0.88[ASN][1000 genomes]
rs2908986	0.82[EUR][1000 genomes]
rs2908988	0.88[CEU][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2908989	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]
rs2908990	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3113988	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4834834	0.88[ASN][1000 genomes]
rs6810690	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7661491	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs903147	0.84[ASN][1000 genomes]
rs972311	0.81[CHB][hapmap];0.80[CHD][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2934379	QRFPR	cis	parietal	SCAN

Chromatin state (count:94 , 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	chr4:120971200-120986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:120971200-120986400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:120971200-120986800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:120971200-120987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:120971200-120987200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:120971200-120987400	Weak transcription	Left Ventricle	heart
9	chr4:120975400-120986800	Weak transcription	Primary B cells from cord blood	blood
10	chr4:120975800-120986800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:120977400-120986600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:120977400-120986600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:120977400-120986800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:120977400-120987200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:120978200-120987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:120978400-120986600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:120979600-120986800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:120981200-120986800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:120981200-120987200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:120981400-120987200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:120982000-120987200	Weak transcription	Fetal Brain Male	brain
22	chr4:120982400-120986200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr4:120982600-120986600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:120983200-120987200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:120983200-120987200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:120983600-120986200	Weak transcription	Fetal Brain Female	brain
27	chr4:120983600-120986400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr4:120983600-120986600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:120983600-120987000	Enhancers	Osteobl	bone
30	chr4:120983800-120986600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr4:120983800-120986800	Enhancers	Fetal Heart	heart
32	chr4:120984000-120986600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:120984200-120986200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:120984400-120986200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:120984400-120986200	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr4:120984400-120986600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:120984600-120987200	Weak transcription	Placenta	Placenta
38	chr4:120984800-120986800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:120985000-120986600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:120985000-120986600	Enhancers	Thymus	Thymus
41	chr4:120985000-120987000	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr4:120985400-120986200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:120985400-120986200	Enhancers	NHDF-Ad	bronchial
44	chr4:120985400-120986400	Flanking Active TSS	HepG2	liver
45	chr4:120985400-120986600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
46	chr4:120985400-120986600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
47	chr4:120985400-120986800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
48	chr4:120985400-120986800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:120985400-120987000	Enhancers	Primary T cells from cord blood	blood
50	chr4:120985400-120987000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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