Variant report

Variant	rs4236093
Chromosome Location	chr6:12957825-12957826
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:12957516-12958294	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr6:12957402-12957869	HUVEC	blood vessel:	n/a	n/a
3	RAD21	chr6:12957798-12958755	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr6:12957820-12957970	HepG2	liver:	n/a	n/a
5	SIN3A	chr6:12957507-12958274	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr6:12957825-12958362	MCF-7	breast:	n/a	chr6:12958035-12958050
7	MXI1	chr6:12957266-12959118	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:12957756-12958149	Gliobla	brain:	n/a	n/a
9	MAX	chr6:12957823-12958340	SK-N-SH	brain:	n/a	chr6:12958035-12958050
10	POLR2A	chr6:12957477-12958503	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr6:12957780-12957930	HRE	kidney:	n/a	n/a
12	EBF1	chr6:12957706-12957923	GM12878	blood:	n/a	n/a
13	MAX	chr6:12957336-12958348	NB4	blood:	n/a	chr6:12958035-12958050

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:12957800-12957850	AG09319	gingival:	n/a
2	chr6:12957800-12957850	GM12892	blood:	n/a
3	chr6:12957800-12957850	AoSMC	blood vessel:	n/a
4	chr6:12957800-12957850	HepG2	liver:	n/a
5	chr6:12957800-12957850	HEK293	kidney:	embryo
6	chr6:12957800-12957850	SKMC	muscle:	n/a
7	chr6:12957800-12957850	HCPEpiC	choroid plexus:	n/a
8	chr6:12957800-12957850	AG04450	lung:	fetal
9	chr6:12957800-12957850	Hepatocyte	liver:	n/a
10	chr6:12957800-12957850	PANC-1	pancreas:	n/a
11	chr6:12957800-12957850	Caco-2	colon:	n/a
12	chr6:12957800-12957850	IMR90	lung:	fetal
13	chr6:12957800-12957850	HNPCEpiC	eye:	n/a
14	chr6:12957800-12957850	PrEC	prostate:	n/a
15	chr6:12957800-12957850	HIPEpiC	eye:	n/a
16	chr6:12957800-12957850	BE2_C	brain:	n/a
17	chr6:12957800-12957850	HCT-116	colon:	n/a
18	chr6:12957800-12957850	HMEC	breast:	n/a
19	chr6:12957800-12957850	T-47D	breast:	n/a
20	chr6:12957800-12957850	GM19239	blood:	n/a
21	chr6:12957800-12957850	RPTEC	kidney:	n/a
22	chr6:12957800-12957850	HRCEpiC	kidney:	n/a
23	chr6:12957800-12957850	ECC-1	luminal epithelium:	n/a
24	chr6:12957800-12957850	H1-hESC	embryonic stem cell:	embryo
25	chr6:12957800-12957850	GM12891	blood:	n/a
26	chr6:12957800-12957850	ovcar-3	ovarian:	n/a
27	chr6:12957800-12957850	SAEC	small airway:	n/a
28	chr6:12957800-12957850	A549	lung:	n/a
29	chr6:12957800-12957850	HAEpiC	amniotic membrane:	n/a
30	chr6:12957800-12957850	MCF-7	breast:	n/a
31	chr6:12957800-12957850	SK-N-SH_RA	brain:	n/a
32	chr6:12957800-12957850	NT2-D1	testis:	n/a
33	chr6:12957800-12957850	U87	brain:	n/a
34	chr6:12957800-12957850	GM06990	blood:	n/a
35	chr6:12957800-12957850	BJ	skin:	n/a
36	chr6:12957800-12957850	HCM	heart:	n/a
37	chr6:12957800-12957850	MCF10A-Er-Src	breast:	n/a
38	chr6:12957800-12957850	SK-N-MC	brain:	n/a
39	chr6:12957800-12957850	HUVEC	blood vessel:	n/a
40	chr6:12957800-12957850	HL-60	blood:	n/a
41	chr6:12957800-12957850	AG04449	skin:	fetal
42	chr6:12957800-12957850	GM12878	blood:	n/a
43	chr6:12957800-12957850	Jurkat	blood:	n/a
44	chr6:12957800-12957850	K562	blood:	n/a
45	chr6:12957800-12957850	CMK	blood:	n/a
46	chr6:12957800-12957850	HPAEpiC	pulmonary alveolar:	n/a
47	chr6:12957800-12957850	PFSK-1	brain:	n/a
48	chr6:12957800-12957850	AG10803	skin:	n/a
49	chr6:12957800-12957850	NH-A	brain:	n/a
50	chr6:12957800-12957850	LNCaP	prostate:	n/a

No data

Variant related genes	Relation type
PHACTR1	TF binding region
PHACTR1	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10948372	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11755825	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11756003	0.92[EUR][1000 genomes]
rs13194360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34175679	0.90[EUR][1000 genomes]
rs35266083	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36049381	0.90[EUR][1000 genomes]
rs4129937	0.88[GIH][hapmap]
rs4331981	0.97[GIH][hapmap]
rs4588689	0.89[EUR][1000 genomes]
rs4715045	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs59778206	0.84[ASN][1000 genomes]
rs62386820	0.91[EUR][1000 genomes]
rs62386821	0.90[EUR][1000 genomes]
rs6458577	0.84[ASN][1000 genomes]
rs66820937	0.92[EUR][1000 genomes]
rs6906017	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6906890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923878	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs6929107	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7757180	0.88[ASN][1000 genomes]
rs7769758	0.88[ASN][1000 genomes]
rs7775566	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7775710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9395336	0.85[GIH][hapmap]
rs9473070	0.86[ASN][1000 genomes]
rs9473082	0.88[ASN][1000 genomes]
rs9473086	0.81[CEU][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv5202	chr6:12916229-12958517	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4236093	HIVEP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12955800-12958800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:12956600-12958400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:12956600-12958400	Active TSS	Primary T cells from cord blood	blood
4	chr6:12956800-12958000	Active TSS	Primary B cells from cord blood	blood
5	chr6:12956800-12959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:12957000-12958000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:12957000-12958000	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:12957000-12958200	Flanking Bivalent TSS/Enh	Dnd41	blood
9	chr6:12957000-12958400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:12957000-12959000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:12957000-12959000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:12957000-12959000	Active TSS	HSMMtube	muscle
13	chr6:12957000-12959000	Active TSS	NHDF-Ad	bronchial
14	chr6:12957000-12959200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:12957000-12959400	Active TSS	Brain Hippocampus Middle	brain
16	chr6:12957000-12960000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:12957200-12958000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr6:12957200-12958000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:12957200-12958000	Active TSS	Primary monocytes fromperipheralblood	blood
20	chr6:12957200-12958000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:12957200-12958000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:12957200-12958200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr6:12957200-12958200	Active TSS	Fetal Lung	lung
24	chr6:12957200-12958200	Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:12957200-12958400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:12957200-12958400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:12957200-12958400	Active TSS	Psoas Muscle	Psoas
28	chr6:12957200-12958400	Active TSS	Small Intestine	intestine
29	chr6:12957200-12958800	Active TSS	Brain Anterior Caudate	brain
30	chr6:12957200-12958800	Active TSS	Ovary	ovary
31	chr6:12957200-12958800	Active TSS	Thymus	Thymus
32	chr6:12957200-12959000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:12957200-12959000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:12957200-12959000	Active TSS	Brain Cingulate Gyrus	brain
35	chr6:12957200-12959200	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr6:12957200-12959200	Active TSS	Right Atrium	heart
37	chr6:12957200-12959200	Active TSS	HSMM	muscle
38	chr6:12957200-12960200	Active TSS	Stomach Smooth Muscle	stomach
39	chr6:12957200-12961400	Active TSS	Aorta	Aorta
40	chr6:12957400-12958000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:12957400-12958000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:12957400-12958000	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:12957400-12958000	Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:12957400-12958000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr6:12957400-12958000	Active TSS	HUVEC	blood vessel
46	chr6:12957400-12958000	Active TSS	NH-A	brain
47	chr6:12957400-12958000	Active TSS	NHEK	skin
48	chr6:12957400-12958200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:12957400-12958200	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:12957400-12958200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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