Variant report

Variant	rs4582838
Chromosome Location	chr1:247373571-247373572
allele	A/C
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	ELK4	chr1:247373368-247374358	Hela-S3	cervix:	n/a	n/a
6	BACH1	chr1:247373481-247373695	K562	blood:	n/a	n/a
7	MXI1	chr1:247372272-247375223	SK-N-SH	brain:	n/a	n/a
8	SIN3AK20	chr1:247373471-247374399	PANC-1	pancreas:	n/a	n/a
9	TAF1	chr1:247373535-247374400	PFSK-1	brain:	n/a	n/a
10	RAD21	chr1:247373487-247374343	IMR90	lung:	n/a	chr1:247373724-247373737 chr1:247373953-247373963
11	MAX	chr1:247373539-247374511	HepG2	liver:	n/a	n/a
12	SIN3A	chr1:247373539-247374361	GM12878	blood:	n/a	chr1:247373744-247373755
13	EP300	chr1:247372831-247374564	K562	blood:	n/a	n/a
14	MAX	chr1:247373536-247374451	A549	lung:	n/a	n/a
15	GABPA	chr1:247373526-247374392	HL-60	blood:	n/a	chr1:247373975-247373984
16	SIN3A	chr1:247373528-247374510	H1-hESC	embryonic stem cell:	n/a	chr1:247373744-247373755
17	E2F4	chr1:247373362-247373598	MCF10A-Er-Src	breast:	n/a	n/a
18	REST	chr1:247373564-247374356	PFSK-1	brain:	n/a	n/a
19	GATA3	chr1:247373520-247374320	A549	lung:	n/a	n/a
20	UBTF	chr1:247373555-247374167	K562	blood:	n/a	n/a
21	RUNX3	chr1:247373428-247374448	GM12878	blood:	n/a	n/a
22	ELK1	chr1:247373570-247374368	GM12878	blood:	n/a	n/a
23	WRNIP1	chr1:247373449-247373757	GM12878	blood:	n/a	n/a
24	JUND	chr1:247373509-247374522	K562	blood:	n/a	n/a
25	ELF1	chr1:247373378-247374651	HCT-116	colon:	n/a	n/a
26	POLR2A	chr1:247373534-247374498	GM19099	blood:	n/a	n/a
27	MAX	chr1:247373531-247374512	K562	blood:	n/a	n/a
28	TCF12	chr1:247373504-247374493	ECC-1	luminal epithelium:	n/a	n/a
29	SMARCB1	chr1:247373544-247374400	Hela-S3	cervix:	n/a	n/a
30	CHD1	chr1:247373371-247374304	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:247373440-247374496	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:247373557-247374388	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr1:247373558-247374500	Hela-S3	cervix:	n/a	n/a
34	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
35	E2F6	chr1:247373403-247374452	A549	lung:	n/a	n/a
36	CBX3	chr1:247373352-247374504	K562	blood:	n/a	n/a
37	SMC3	chr1:247373551-247374437	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:247372902-247374438	Hela-S3	cervix:	n/a	n/a
39	MAX	chr1:247373504-247374442	Hela-S3	cervix:	n/a	n/a
40	MAX	chr1:247373509-247374481	MCF-7	breast:	n/a	n/a
41	ZBTB7A	chr1:247373455-247374111	K562	blood:	n/a	n/a
42	HCFC1	chr1:247373226-247374696	Hela-S3	cervix:	n/a	n/a
43	TEAD4	chr1:247373489-247374333	K562	blood:	n/a	n/a
44	POLR2A	chr1:247373548-247374462	K562	blood:	n/a	n/a
45	MYC	chr1:247373411-247374460	NB4	blood:	n/a	n/a
46	RAD21	chr1:247373569-247374232	H1-hESC	embryonic stem cell:	n/a	chr1:247373724-247373737 chr1:247373953-247373963
47	NR2F2	chr1:247373358-247374644	K562	blood:	n/a	chr1:247374490-247374505
48	ELF1	chr1:247373514-247374510	MCF-7	breast:	n/a	n/a
49	TCF12	chr1:247373428-247374450	A549	lung:	n/a	n/a
50	POLR2A	chr1:247373428-247374585	PFSK-1	brain:	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	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
4	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
5	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
6	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:

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

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10924964	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1115202	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12567626	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12569042	0.83[CEU][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17269923	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2380117	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2892054	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35229190	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3738443	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41315860	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4269806	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4351686	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4551629	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55643126	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55914345	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56029850	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56046175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56065612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56340510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58405512	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60240280	0.83[EUR][1000 genomes]
rs60698393	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61839991	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61839994	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61839996	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61839997	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61840000	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61840048	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61840053	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61840054	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840055	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840056	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840057	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656425	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6660351	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6665647	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6666543	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6668154	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6680197	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6684181	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6698690	0.86[EUR][1000 genomes]
rs74152976	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7536883	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7546908	0.83[CEU][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7551871	0.83[CEU][hapmap];0.86[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4582838	RP11-488L18.10	cis	Artery Tibial	GTEx
rs4582838	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx
rs4582838	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	chr1:247372000-247373600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:247372200-247373600	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr1:247372200-247373600	Flanking Active TSS	Hela-S3	cervix
4	chr1:247372400-247373600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:247372400-247373600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr1:247372400-247373600	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr1:247372400-247373600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:247372400-247373800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:247372400-247373800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr1:247372600-247373600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:247372600-247373600	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr1:247372600-247373600	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr1:247372600-247373600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:247372600-247373600	Flanking Active TSS	Fetal Brain Male	brain
15	chr1:247372600-247373600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr1:247372600-247373800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr1:247372600-247373800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:247372600-247373800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:247372600-247374200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:247372600-247374200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:247372600-247374400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:247372600-247374600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:247372800-247373600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:247372800-247373600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:247372800-247373600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr1:247372800-247373600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr1:247372800-247373600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:247372800-247373600	Flanking Active TSS	HUVEC	blood vessel
29	chr1:247372800-247373600	Flanking Active TSS	Osteobl	bone
30	chr1:247372800-247373800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr1:247372800-247373800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr1:247372800-247374000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:247372800-247374200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:247372800-247374400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:247372800-247374400	Active TSS	HSMM	muscle
36	chr1:247372800-247374600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:247373000-247373600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:247373000-247373600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:247373000-247373600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr1:247373000-247373600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:247373000-247373600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr1:247373000-247373600	Flanking Active TSS	Fetal Heart	heart
43	chr1:247373000-247373600	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr1:247373000-247373600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr1:247373000-247373600	Weak transcription	Spleen	Spleen
46	chr1:247373000-247373600	Flanking Active TSS	Dnd41	blood
47	chr1:247373000-247373800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr1:247373000-247373800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:247373000-247373800	Active TSS	Right Atrium	heart
50	chr1:247373000-247374200	Active TSS	HUES6 Cell Line	embryonic stem cell

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