Variant report

Variant	rs58826561
Chromosome Location	chr1:213124303-213124304
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	chr1:213123559-213124674	GM12878	blood:	n/a	n/a
2	CTCF	chr1:213124180-213124330	HCM	heart:	n/a	n/a
3	MAX	chr1:213124054-213124424	MCF-7	breast:	n/a	n/a
4	MAX	chr1:213123490-213124532	MCF-7	breast:	n/a	n/a
5	MAX	chr1:213123481-213124735	ECC-1	luminal epithelium:	n/a	n/a
6	USF2	chr1:213124128-213124637	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:213124180-213124330	GM12878	blood:	n/a	n/a
8	CTCF	chr1:213124203-213124376	GM19238	blood:	n/a	n/a
9	CTCF	chr1:213124233-213124365	GM19239	blood:	n/a	n/a
10	CTCF	chr1:213124118-213124812	GM12878	blood:	n/a	n/a
11	MXI1	chr1:213123580-213125272	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:213123485-213125219	GM19193	blood:	n/a	n/a
13	CTCF	chr1:213124180-213124330	GM12864	blood:	n/a	n/a
14	CTCF	chr1:213124160-213124310	GM12871	blood:	n/a	n/a
15	POLR2A	chr1:213123469-213125260	H1-neurons	neurons:	n/a	n/a
16	CTCF	chr1:213124180-213124330	GM12866	blood:	n/a	n/a
17	POLR2A	chr1:213123537-213124698	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:213124180-213124330	GM12870	blood:	n/a	n/a
19	ZBTB7A	chr1:213123949-213124713	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr1:213124055-213124518	H1-hESC	embryonic stem cell:	n/a	n/a
21	STAT5A	chr1:213123801-213124633	GM12878	blood:	n/a	chr1:213124225-213124234 chr1:213124224-213124233
22	POLR2A	chr1:213123557-213124437	GM15510	blood:	n/a	n/a
23	MXI1	chr1:213123173-213125500	SK-N-SH	brain:	n/a	n/a
24	TBP	chr1:213124298-213124310	GM12878	blood:	n/a	n/a
25	TEAD4	chr1:213123533-213124584	ECC-1	luminal epithelium:	n/a	chr1:213124348-213124357
26	CTCF	chr1:213124180-213124330	GM12874	blood:	n/a	n/a
27	CTBP2	chr1:213123605-213125255	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3A	chr1:213123271-213126305	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr1:213123723-213124612	H1-neurons	neurons:	n/a	n/a
30	TCF12	chr1:213124079-213124850	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr1:213124260-213124410	HA-sp	spinal cord:	n/a	n/a
32	CTCF	chr1:213124200-213124350	GM12867	blood:	n/a	n/a
33	MAX	chr1:213123405-213124518	A549	lung:	n/a	n/a
34	MAX	chr1:213124267-213124324	HepG2	liver:	n/a	n/a
35	CTCF	chr1:213124180-213124330	GM12865	blood:	n/a	n/a
36	CTCF	chr1:213124220-213124370	GM12865	blood:	n/a	n/a
37	RCOR1	chr1:213123607-213124490	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:213123461-213124843	GM19099	blood:	n/a	n/a
39	POLR2A	chr1:213123450-213124795	GM12892	blood:	n/a	n/a
40	HA-E2F1	chr1:213123435-213124453	MCF-7	breast:	n/a	chr1:213124115-213124124 chr1:213123797-213123806
41	CTCF	chr1:213124240-213124390	WERI-Rb-1	eye:	n/a	n/a
42	POLR2A	chr1:213123456-213124426	GM12878	blood:	n/a	n/a
43	CTCF	chr1:213124240-213124390	GM12871	blood:	n/a	n/a
44	CTCF	chr1:213124200-213124350	HPAF	blood vessel:	n/a	n/a
45	BHLHE40	chr1:213123506-213124663	GM12878	blood:	n/a	n/a
46	E2F6	chr1:213123540-213124525	H1-hESC	embryonic stem cell:	n/a	chr1:213124115-213124124 chr1:213123797-213123806
47	CTCF	chr1:213124200-213124350	SK-N-SH_RA	brain:	n/a	n/a
48	MAX	chr1:213123421-213124649	ECC-1	luminal epithelium:	n/a	n/a
49	STAT1	chr1:213123513-213124425	GM12878	blood:	n/a	chr1:213124225-213124234 chr1:213124224-213124233
50	MAX	chr1:213123579-213124482	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
VASH2	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10127459	0.80[EUR][1000 genomes]
rs12563331	0.91[ASN][1000 genomes]
rs17020046	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57244386	0.91[ASN][1000 genomes]
rs59252582	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59579946	0.91[ASN][1000 genomes]
rs59870594	0.91[ASN][1000 genomes]
rs6656706	0.97[EUR][1000 genomes]
rs6656738	0.89[EUR][1000 genomes]
rs6667192	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674283	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6680470	0.97[EUR][1000 genomes]
rs903802	0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213123000-213125000	Active TSS	Brain Cingulate Gyrus	brain
2	chr1:213123200-213124400	Active TSS	A549	lung
3	chr1:213123200-213124800	Bivalent Enhancer	Spleen	Spleen
4	chr1:213123200-213125000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:213123200-213125200	Active TSS	Brain Hippocampus Middle	brain
6	chr1:213123200-213125400	Active TSS	Fetal Brain Male	brain
7	chr1:213123200-213125400	Active TSS	Fetal Brain Female	brain
8	chr1:213123400-213124400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
9	chr1:213123400-213124400	Active TSS	Right Atrium	heart
10	chr1:213123400-213124400	Active TSS	Thymus	Thymus
11	chr1:213123400-213124400	Bivalent/Poised TSS	K562	blood
12	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
14	chr1:213123400-213124800	Active TSS	Psoas Muscle	Psoas
15	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
16	chr1:213123400-213125000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:213123400-213125000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:213123400-213125000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:213123400-213125000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:213123400-213125000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:213123400-213125000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:213123400-213125000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:213123400-213125000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:213123400-213125000	Active TSS	Esophagus	oesophagus
25	chr1:213123400-213125000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:213123400-213125000	Bivalent/Poised TSS	NHLF	lung
27	chr1:213123400-213125200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:213123400-213125200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:213123400-213125200	Active TSS	Brain Angular Gyrus	brain
33	chr1:213123400-213125200	Active TSS	Fetal Lung	lung
34	chr1:213123400-213125400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:213123400-213125400	Active TSS	Fetal Kidney	kidney
36	chr1:213123400-213125400	Active TSS	HSMMtube	muscle
37	chr1:213123400-213125600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:213123400-213125600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:213123400-213125800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:213123600-213124400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:213123600-213124400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:213123600-213124400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:213123600-213124400	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:213123600-213124600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Placenta	Placenta
48	chr1:213123600-213124800	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:213123600-213124800	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:213123600-213124800	Active TSS	Brain Substantia Nigra	brain

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