Variant report

Variant	rs59252582
Chromosome Location	chr1:213124428-213124429
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	POLR2A	chr1:213123559-213124674	GM12878	blood:	n/a	n/a
2	MAX	chr1:213123490-213124532	MCF-7	breast:	n/a	n/a
3	MAX	chr1:213123481-213124735	ECC-1	luminal epithelium:	n/a	n/a
4	USF2	chr1:213124128-213124637	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:213124118-213124812	GM12878	blood:	n/a	n/a
6	MXI1	chr1:213123580-213125272	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:213123485-213125219	GM19193	blood:	n/a	n/a
8	POLR2A	chr1:213123469-213125260	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr1:213123537-213124698	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZBTB7A	chr1:213123949-213124713	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr1:213124055-213124518	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT5A	chr1:213123801-213124633	GM12878	blood:	n/a	chr1:213124225-213124234 chr1:213124224-213124233
13	POLR2A	chr1:213123557-213124437	GM15510	blood:	n/a	n/a
14	MXI1	chr1:213123173-213125500	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr1:213123533-213124584	ECC-1	luminal epithelium:	n/a	chr1:213124348-213124357
16	CTBP2	chr1:213123605-213125255	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3A	chr1:213123271-213126305	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr1:213123723-213124612	H1-neurons	neurons:	n/a	n/a
19	TCF12	chr1:213124079-213124850	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr1:213123405-213124518	A549	lung:	n/a	n/a
21	RCOR1	chr1:213123607-213124490	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:213123461-213124843	GM19099	blood:	n/a	n/a
23	POLR2A	chr1:213123450-213124795	GM12892	blood:	n/a	n/a
24	HA-E2F1	chr1:213123435-213124453	MCF-7	breast:	n/a	chr1:213124115-213124124 chr1:213123797-213123806
25	BHLHE40	chr1:213123506-213124663	GM12878	blood:	n/a	n/a
26	E2F6	chr1:213123540-213124525	H1-hESC	embryonic stem cell:	n/a	chr1:213124115-213124124 chr1:213123797-213123806
27	MAX	chr1:213123421-213124649	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr1:213123579-213124482	HepG2	liver:	n/a	n/a
29	MAX	chr1:213123502-213124685	GM12878	blood:	n/a	n/a
30	SMARCB1	chr1:213123531-213124633	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr1:213123506-213124848	H1-neurons	neurons:	n/a	n/a
32	CHD1	chr1:213123771-213124610	GM12878	blood:	n/a	chr1:213124579-213124589
33	TEAD4	chr1:213124197-213124510	H1-hESC	embryonic stem cell:	n/a	chr1:213124348-213124357
34	TEAD4	chr1:213123815-213124598	ECC-1	luminal epithelium:	n/a	chr1:213124348-213124357
35	CTCF	chr1:213124320-213124470	GM12873	blood:	n/a	n/a
36	POLR2A	chr1:213123435-213124706	GM12878	blood:	n/a	n/a
37	MAX	chr1:213123528-213124548	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr1:213124407-213124459	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr1:213124400-213124550	GM12878	blood:	n/a	n/a
40	MTA3	chr1:213123114-213124782	GM12878	blood:	n/a	n/a
41	RUNX3	chr1:213124220-213124842	GM12878	blood:	n/a	n/a
42	MAX	chr1:213123459-213124648	SK-N-SH	brain:	n/a	n/a
43	WRNIP1	chr1:213124277-213124667	GM12878	blood:	n/a	n/a
44	TEAD4	chr1:213123930-213124455	H1-hESC	embryonic stem cell:	n/a	chr1:213124348-213124357
45	MAZ	chr1:213123408-213125227	IMR90	lung:	n/a	n/a
46	CTCF	chr1:213124360-213124510	RPTEC	kidney:	n/a	n/a
47	POLR2A	chr1:213123783-213124628	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr1:213124280-213124430	GM12869	blood:	n/a	n/a
49	MAX	chr1:213124101-213124507	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF12	chr1:213123579-213124583	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
VASH2	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127459	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746436	1.00[ASN][1000 genomes]
rs10779594	1.00[ASN][1000 genomes]
rs10864003	1.00[ASN][1000 genomes]
rs10864019	1.00[ASN][1000 genomes]
rs11120033	1.00[ASN][1000 genomes]
rs12036735	1.00[ASN][1000 genomes]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs1615680	1.00[ASN][1000 genomes]
rs1692178	1.00[ASN][1000 genomes]
rs1692179	1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17020044	1.00[ASN][1000 genomes]
rs17020046	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770777	1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	1.00[ASN][1000 genomes]
rs2047289	1.00[ASN][1000 genomes]
rs2047293	1.00[ASN][1000 genomes]
rs2359324	1.00[ASN][1000 genomes]
rs2644545	1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[ASN][1000 genomes]
rs2792561	1.00[ASN][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4951649	1.00[ASN][1000 genomes]
rs58826561	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6540768	1.00[ASN][1000 genomes]
rs6656706	0.92[EUR][1000 genomes]
rs6656738	0.93[EUR][1000 genomes]
rs6666362	1.00[ASN][1000 genomes]
rs6667161	1.00[ASN][1000 genomes]
rs6667192	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6674283	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6674933	1.00[ASN][1000 genomes]
rs6680470	0.92[EUR][1000 genomes]
rs6689134	1.00[ASN][1000 genomes]
rs6703612	1.00[ASN][1000 genomes]
rs7528119	1.00[ASN][1000 genomes]
rs7533932	1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs903802	0.97[EUR][1000 genomes]
rs963327	1.00[ASN][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:123 , 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	chr1:213123200-213124800	Bivalent Enhancer	Spleen	Spleen
3	chr1:213123200-213125000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:213123200-213125200	Active TSS	Brain Hippocampus Middle	brain
5	chr1:213123200-213125400	Active TSS	Fetal Brain Male	brain
6	chr1:213123200-213125400	Active TSS	Fetal Brain Female	brain
7	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
8	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr1:213123400-213124800	Active TSS	Psoas Muscle	Psoas
10	chr1:213123400-213124800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr1:213123400-213125000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr1:213123400-213125000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:213123400-213125000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:213123400-213125000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:213123400-213125000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:213123400-213125000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:213123400-213125000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:213123400-213125000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:213123400-213125000	Active TSS	Esophagus	oesophagus
20	chr1:213123400-213125000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:213123400-213125000	Bivalent/Poised TSS	NHLF	lung
22	chr1:213123400-213125200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:213123400-213125200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:213123400-213125200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:213123400-213125200	Active TSS	Brain Angular Gyrus	brain
28	chr1:213123400-213125200	Active TSS	Fetal Lung	lung
29	chr1:213123400-213125400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:213123400-213125400	Active TSS	Fetal Kidney	kidney
31	chr1:213123400-213125400	Active TSS	HSMMtube	muscle
32	chr1:213123400-213125600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:213123400-213125600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:213123400-213125800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
36	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:213123600-213124600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:213123600-213124600	Flanking Bivalent TSS/Enh	Placenta	Placenta
39	chr1:213123600-213124800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:213123600-213124800	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:213123600-213124800	Active TSS	Brain Substantia Nigra	brain
42	chr1:213123600-213125000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:213123600-213125000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:213123600-213125000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:213123600-213125000	Bivalent/Poised TSS	Fetal Stomach	stomach
46	chr1:213123600-213125000	Active TSS	Gastric	stomach
47	chr1:213123600-213125000	Active TSS	Left Ventricle	heart
48	chr1:213123600-213125000	Active TSS	Placenta Amnion	Placenta Amnion
49	chr1:213123600-213125200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:213123600-213125200	Active TSS	Aorta	Aorta

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