Variant report

Variant	rs4658100
Chromosome Location	chr1:91965767-91965768
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	chr1:91965297-91967439	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:91965502-91967438	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:91965298-91968039	H1-hESC	embryonic stem cell:	n/a	n/a
4	KAP1	chr1:91965606-91967313	U2OS	brain:	n/a	n/a
5	POLR2A	chr1:91965700-91967369	GM18526	blood:	n/a	n/a
6	POLR2A	chr1:91965536-91967735	K562	blood:	n/a	n/a
7	TEAD4	chr1:91965407-91967436	K562	blood:	n/a	n/a
8	STAT1	chr1:91965457-91967328	Hela-S3	cervix:	n/a	chr1:91966200-91966214 chr1:91966273-91966281 chr1:91966197-91966217 chr1:91966203-91966212 chr1:91966201-91966212 chr1:91966202-91966211
9	MAFK	chr1:91963040-91970259	HepG2	liver:	n/a	chr1:91966021-91966035 chr1:91968577-91968588
10	POLR2A	chr1:91965435-91967433	HL-60	blood:	n/a	n/a
11	POLR2A	chr1:91965454-91965775	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOSL2	chr1:91964801-91967404	HepG2	liver:	n/a	chr1:91966158-91966170 chr1:91966078-91966087 chr1:91966604-91966613
13	POLR2A	chr1:91965080-91967612	GM12878	blood:	n/a	n/a
14	STAT3	chr1:91965766-91967927	MCF10A-Er-Src	breast:	n/a	chr1:91966200-91966214 chr1:91966273-91966281 chr1:91966197-91966217 chr1:91966201-91966212 chr1:91966203-91966212 chr1:91966202-91966211
15	POLR2A	chr1:91965417-91967513	K562	blood:	n/a	n/a
16	MAZ	chr1:91965281-91967494	IMR90	lung:	n/a	n/a
17	POLR2A	chr1:91965663-91967438	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:91965509-91967868	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:91965463-91967344	HL-60	blood:	n/a	n/a
20	E2F6	chr1:91965517-91967314	K562	blood:	n/a	chr1:91966631-91966643 chr1:91966600-91966609 chr1:91966302-91966314 chr1:91966648-91966657 chr1:91966599-91966610 chr1:91966393-91966403 chr1:91966635-91966642 chr1:91966601-91966608 chr1:91966601-91966608 chr1:91966596-91966611 chr1:91966635-91966642 chr1:91966376-91966385 chr1:91966395-91966407 chr1:91966600-91966612 chr1:91966635-91966642 chr1:91966632-91966643 chr1:91966411-91966420 chr1:91966601-91966608
21	TAF1	chr1:91965437-91965852	H1-hESC	embryonic stem cell:	n/a	n/a
22	TBL1XR1	chr1:91965626-91967262	K562	blood:	n/a	n/a
23	GATA1	chr1:91965569-91968164	PBDE	blood:	n/a	chr1:91967672-91967693 chr1:91967680-91967697 chr1:91967679-91967686 chr1:91966077-91966087 chr1:91967675-91967691 chr1:91967678-91967688 chr1:91967679-91967686 chr1:91967679-91967686 chr1:91967676-91967686
24	POLR2A	chr1:91965419-91967285	K562	blood:	n/a	n/a
25	ZKSCAN1	chr1:91965644-91965919	Hela-S3	cervix:	n/a	n/a
26	JUND	chr1:91963265-91969107	HepG2	liver:	n/a	chr1:91966158-91966170 chr1:91967689-91967697 chr1:91966078-91966087 chr1:91966604-91966613 chr1:91968312-91968321 chr1:91968136-91968145
27	SPI1	chr1:91965549-91965803	K562	blood:	n/a	n/a
28	IRF1	chr1:91965454-91968027	K562	blood:	n/a	chr1:91967651-91967667 chr1:91967658-91967668
29	POLR2A	chr1:91965509-91967275	NB4	blood:	n/a	n/a
30	MYC	chr1:91965657-91967421	K562	blood:	n/a	chr1:91967048-91967058
31	IRF1	chr1:91965283-91967752	K562	blood:	n/a	chr1:91967651-91967667 chr1:91967658-91967668
32	POLR2A	chr1:91965623-91967344	GM19099	blood:	n/a	n/a
33	POLR2A	chr1:91965539-91967430	Hela-S3	cervix:	n/a	n/a
34	FOSL2	chr1:91962979-91969220	HepG2	liver:	n/a	chr1:91966158-91966170 chr1:91967689-91967697 chr1:91966078-91966087 chr1:91966604-91966613 chr1:91968312-91968321 chr1:91968136-91968145
35	ZNF143	chr1:91965499-91967335	K562	blood:	n/a	n/a
36	RFX5	chr1:91965563-91967031	HepG2	liver:	n/a	n/a
37	ZBTB33	chr1:91965545-91966394	HepG2	liver:	n/a	n/a
38	RCOR1	chr1:91964349-91967276	HepG2	liver:	n/a	n/a
39	TAL1	chr1:91965729-91968223	K562	blood:	n/a	chr1:91967679-91967697
40	PML	chr1:91965756-91967175	K562	blood:	n/a	n/a
41	POLR2A	chr1:91965759-91967351	Hela-S3	cervix:	n/a	n/a
42	PML	chr1:91965504-91967223	K562	blood:	n/a	n/a
43	CTCF	chr1:91965705-91967577	SK-N-SH	brain:	n/a	n/a
44	MYC	chr1:91965472-91967381	NB4	blood:	n/a	chr1:91967048-91967058
45	POLR2A	chr1:91965585-91967217	K562	blood:	n/a	n/a
46	POLR2A	chr1:91965599-91967439	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr1:91965659-91967394	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr1:91965469-91967440	K562	blood:	n/a	n/a
49	POLR2A	chr1:91965574-91967917	PBDE	blood:	n/a	n/a
50	SPI1	chr1:91965379-91965928	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:91869685..91873685-chr1:91965673..91969192,5	K562	blood:
2	chr1:91867702..91872217-chr1:91965179..91968319,5	K562	blood:
3	chr1:91870066..91871690-chr1:91965545..91967764,2	MCF-7	breast:

Variant related genes	Relation type
CDC7	TF binding region
ENSG00000162669	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11164872	0.92[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164900	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs494244	0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs565451	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7536200	0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91956600-91965800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:91965000-91965800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:91965200-91966600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:91965400-91965800	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:91965400-91965800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:91965400-91966200	Flanking Active TSS	K562	blood
7	chr1:91965400-91966400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:91965400-91966400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:91965400-91966400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:91965600-91965800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:91965600-91965800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:91965600-91965800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:91965600-91965800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:91965600-91965800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:91965600-91965800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:91965600-91965800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:91965600-91965800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:91965600-91965800	Enhancers	Primary T cells from cord blood	blood
19	chr1:91965600-91965800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:91965600-91965800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:91965600-91965800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:91965600-91965800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:91965600-91965800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:91965600-91965800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:91965600-91965800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:91965600-91965800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:91965600-91965800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:91965600-91965800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:91965600-91965800	Enhancers	Adipose Nuclei	Adipose
30	chr1:91965600-91965800	Enhancers	Liver	Liver
31	chr1:91965600-91965800	Active TSS	Brain Angular Gyrus	brain
32	chr1:91965600-91965800	Enhancers	Brain Germinal Matrix	brain
33	chr1:91965600-91965800	Enhancers	Brain Substantia Nigra	brain
34	chr1:91965600-91965800	Enhancers	Colon Smooth Muscle	Colon
35	chr1:91965600-91965800	Enhancers	Fetal Brain Male	brain
36	chr1:91965600-91965800	Enhancers	Fetal Brain Female	brain
37	chr1:91965600-91965800	Enhancers	Fetal Heart	heart
38	chr1:91965600-91965800	Enhancers	Fetal Intestine Large	intestine
39	chr1:91965600-91965800	Enhancers	Fetal Kidney	kidney
40	chr1:91965600-91965800	Enhancers	Fetal Muscle Leg	muscle
41	chr1:91965600-91965800	Enhancers	Fetal Stomach	stomach
42	chr1:91965600-91965800	Enhancers	Fetal Thymus	thymus
43	chr1:91965600-91965800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:91965600-91965800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:91965600-91965800	Enhancers	Small Intestine	intestine
46	chr1:91965600-91965800	Enhancers	Stomach Smooth Muscle	stomach
47	chr1:91965600-91965800	Enhancers	Thymus	Thymus
48	chr1:91965600-91965800	Enhancers	A549	lung
49	chr1:91965600-91965800	Active TSS	GM12878-XiMat	blood
50	chr1:91965600-91965800	Enhancers	NH-A	brain

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