Variant report

Variant	rs4314914
Chromosome Location	chr1:247373628-247373629
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	SIN3AK20	chr1:247373512-247374468	HCT-116	colon:	n/a	n/a
2	MXI1	chr1:247373356-247374638	IMR90	lung:	n/a	n/a
3	CREB1	chr1:247373528-247374543	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr1:247373239-247374467	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:247373586-247374412	HUVEC	blood vessel:	n/a	n/a
6	ELK4	chr1:247373368-247374358	Hela-S3	cervix:	n/a	n/a
7	BACH1	chr1:247373481-247373695	K562	blood:	n/a	n/a
8	MXI1	chr1:247373582-247374485	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr1:247372272-247375223	SK-N-SH	brain:	n/a	n/a
10	TAF1	chr1:247373591-247373903	SK-N-SH	brain:	n/a	n/a
11	SIN3AK20	chr1:247373471-247374399	PANC-1	pancreas:	n/a	n/a
12	TAF1	chr1:247373535-247374400	PFSK-1	brain:	n/a	n/a
13	RAD21	chr1:247373487-247374343	IMR90	lung:	n/a	chr1:247373724-247373737 chr1:247373953-247373963
14	POLR2A	chr1:247373573-247374483	Hela-S3	cervix:	n/a	n/a
15	STAT5A	chr1:247373607-247374210	GM12878	blood:	n/a	n/a
16	MAX	chr1:247373539-247374511	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:247373614-247374399	A549	lung:	n/a	n/a
18	SIN3A	chr1:247373539-247374361	GM12878	blood:	n/a	chr1:247373744-247373755
19	TAF1	chr1:247373572-247374489	K562	blood:	n/a	n/a
20	EP300	chr1:247372831-247374564	K562	blood:	n/a	n/a
21	MAX	chr1:247373536-247374451	A549	lung:	n/a	n/a
22	GABPA	chr1:247373526-247374392	HL-60	blood:	n/a	chr1:247373975-247373984
23	SIN3A	chr1:247373528-247374510	H1-hESC	embryonic stem cell:	n/a	chr1:247373744-247373755
24	EGR1	chr1:247373591-247374039	GM12878	blood:	n/a	chr1:247373685-247373696 chr1:247373685-247373695 chr1:247373684-247373697 chr1:247373683-247373697 chr1:247373685-247373696 chr1:247373685-247373695
25	REST	chr1:247373564-247374356	PFSK-1	brain:	n/a	n/a
26	YY1	chr1:247373605-247373951	GM12892	blood:	n/a	chr1:247373815-247373829
27	GATA3	chr1:247373520-247374320	A549	lung:	n/a	n/a
28	UBTF	chr1:247373555-247374167	K562	blood:	n/a	n/a
29	RUNX3	chr1:247373428-247374448	GM12878	blood:	n/a	n/a
30	MAZ	chr1:247373575-247374371	Hela-S3	cervix:	n/a	n/a
31	ELK1	chr1:247373570-247374368	GM12878	blood:	n/a	n/a
32	BHLHE40	chr1:247373588-247374484	GM12878	blood:	n/a	chr1:247373721-247373737
33	WRNIP1	chr1:247373449-247373757	GM12878	blood:	n/a	n/a
34	JUND	chr1:247373509-247374522	K562	blood:	n/a	n/a
35	GABPA	chr1:247373588-247374373	K562	blood:	n/a	chr1:247373975-247373984
36	ELF1	chr1:247373378-247374651	HCT-116	colon:	n/a	n/a
37	POLR2A	chr1:247373534-247374498	GM19099	blood:	n/a	n/a
38	TAF1	chr1:247373591-247374389	K562	blood:	n/a	n/a
39	MAX	chr1:247373531-247374512	K562	blood:	n/a	n/a
40	TCF12	chr1:247373504-247374493	ECC-1	luminal epithelium:	n/a	n/a
41	SMARCB1	chr1:247373544-247374400	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr1:247373577-247374375	HepG2	liver:	n/a	n/a
43	CHD1	chr1:247373371-247374304	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:247373440-247374496	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAF1	chr1:247373589-247374533	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr1:247373557-247374388	ECC-1	luminal epithelium:	n/a	n/a
47	GABPA	chr1:247373612-247373989	Hela-S3	cervix:	n/a	chr1:247373975-247373984
48	POLR2A	chr1:247373558-247374500	Hela-S3	cervix:	n/a	n/a
49	EGR1	chr1:247373526-247374383	K562	blood:	n/a	chr1:247373685-247373696 chr1:247373685-247373695 chr1:247373684-247373697 chr1:247373683-247373697 chr1:247373685-247373696 chr1:247373685-247373695
50	E2F6	chr1:247373403-247374452	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
2	chr1:247373468..247374174-chr2:68479757..68480421,2	Hela-S3	cervix:
3	chr1:247373611..247374330-chr11:47429734..47430575,2	Hela-S3	cervix:
4	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
5	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
6	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
7	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:

Variant related genes	Relation type
MIR3916	TF binding region
ENSG00000273064	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000252516	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000221953	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11811599	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1343544	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55768801	0.87[EUR][1000 genomes]
rs56338561	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57861883	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60050650	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61636449	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6680707	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691539	0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6693807	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699577	0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6704060	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4314914	MIR3916	cis	Whole Blood	GTEx
rs4314914	RP11-488L18.10	cis	Artery Tibial	GTEx
rs4314914	LOC729806	Cis_1M	lymphoblastoid	RTeQTL
rs4314914	RP11-488L18.10	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247372400-247373800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:247372400-247373800	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:247372600-247373800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr1:247372600-247373800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:247372600-247373800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:247372600-247374200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:247372600-247374200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:247372600-247374400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:247372600-247374600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:247372800-247373800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr1:247372800-247373800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr1:247372800-247374000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:247372800-247374200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:247372800-247374400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:247372800-247374400	Active TSS	HSMM	muscle
16	chr1:247372800-247374600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:247373000-247373800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr1:247373000-247373800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:247373000-247373800	Active TSS	Right Atrium	heart
20	chr1:247373000-247374200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:247373000-247374200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:247373000-247374200	Active TSS	Fetal Thymus	thymus
23	chr1:247373000-247374200	Active TSS	Lung	lung
24	chr1:247373000-247374200	Active TSS	Pancreas	Pancrea
25	chr1:247373000-247374200	Active TSS	Psoas Muscle	Psoas
26	chr1:247373000-247374200	Active TSS	Right Ventricle	heart
27	chr1:247373000-247374200	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr1:247373000-247374400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:247373000-247374400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:247373000-247374400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:247373000-247374400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:247373000-247374400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:247373000-247374400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:247373000-247374400	Active TSS	Ovary	ovary
35	chr1:247373000-247374400	Active TSS	A549	lung
36	chr1:247373000-247374400	Active TSS	NHDF-Ad	bronchial
37	chr1:247373000-247374600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:247373000-247374600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:247373000-247374600	Active TSS	GM12878-XiMat	blood
40	chr1:247373200-247374200	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:247373200-247374200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:247373200-247374200	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:247373200-247374400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:247373200-247374400	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr1:247373200-247374400	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:247373200-247374400	Active TSS	Fetal Intestine Small	intestine
47	chr1:247373200-247374400	Active TSS	Fetal Kidney	kidney
48	chr1:247373200-247374400	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:247373200-247374400	Active TSS	HSMMtube	muscle
50	chr1:247373200-247374600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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