Variant report

Variant	rs74138596
Chromosome Location	chr1:212803539-212803540
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	MYC	chr1:212803486-212803684	MCF10A-Er-Src	breast:	n/a	n/a
2	USF2	chr1:212803379-212803651	H1-hESC	embryonic stem cell:	n/a	n/a
3	WRNIP1	chr1:212803287-212803654	GM12878	blood:	n/a	n/a
4	CTCF	chr1:212803500-212803650	WERI-Rb-1	eye:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
5	ELF1	chr1:212803326-212803951	GM12878	blood:	n/a	n/a
6	RFX5	chr1:212803463-212803663	HepG2	liver:	n/a	n/a
7	CTCF	chr1:212803480-212803630	HCPEpiC	choroid plexus:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
8	CTCF	chr1:212803374-212803745	ECC-1	luminal epithelium:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
9	CTCF	chr1:212803480-212803630	AG10803	skin:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
10	EBF1	chr1:212803520-212803824	GM12878	blood:	n/a	n/a
11	RAD21	chr1:212803348-212803743	GM12878	blood:	n/a	chr1:212803727-212803739 chr1:212803416-212803430
12	CTCF	chr1:212803445-212803703	Hela-S3	cervix:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
13	CTCF	chr1:212803445-212803707	GM13977	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
14	RAD21	chr1:212803417-212803631	K562	blood:	n/a	n/a
15	RAD21	chr1:212803310-212803774	SK-N-SH_RA	brain:	n/a	chr1:212803727-212803739 chr1:212803416-212803430
16	CTCF	chr1:212803480-212803630	BJ	skin:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
17	RAD21	chr1:212803313-212803768	H1-hESC	embryonic stem cell:	n/a	chr1:212803727-212803739 chr1:212803416-212803430
18	CTCF	chr1:212803480-212803630	HMEC	breast:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
19	CTCF	chr1:212803476-212803687	GM20000	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
20	CTCF	chr1:212803460-212803610	HFF-Myc	foreskin:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
21	CTCF	chr1:212803500-212803650	HRE	kidney:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
22	CEBPB	chr1:212803436-212803635	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:212803319-212803707	H1-hESC	embryonic stem cell:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
24	SPI1	chr1:212803382-212803836	GM12878	blood:	n/a	chr1:212803639-212803652
25	CTCF	chr1:212803480-212803630	GM12878	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
26	SMC3	chr1:212803007-212803936	SK-N-SH	brain:	n/a	chr1:212803565-212803572
27	CTCF	chr1:212803480-212803630	HEK293	kidney:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
28	CTCF	chr1:212803520-212803670	AG04450	lung:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
29	MAFK	chr1:212803489-212803761	K562	blood:	n/a	chr1:212803672-212803681
30	CTCF	chr1:212803451-212803701	A549	lung:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
31	CTCF	chr1:212803439-212803715	T-47D	breast:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
32	CTCF	chr1:212803386-212803763	GM12891	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
33	CTCF	chr1:212803460-212803610	HCT-116	colon:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
34	RAD21	chr1:212803260-212803816	SK-N-SH	brain:	n/a	chr1:212803727-212803739 chr1:212803416-212803430
35	CTCF	chr1:212803500-212803650	GM12870	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
36	FOS	chr1:212803486-212803696	MCF10A-Er-Src	breast:	n/a	chr1:212803542-212803549
37	RAD21	chr1:212803357-212803707	H1-hESC	embryonic stem cell:	n/a	chr1:212803416-212803430
38	CTCF	chr1:212803500-212803650	NHDF-neo	bronchial:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
39	CTCF	chr1:212803500-212803650	RPTEC	kidney:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
40	CTCF	chr1:212803390-212803748	GM19238	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
41	JUND	chr1:212803421-212803789	K562	blood:	n/a	chr1:212803542-212803549
42	CTCF	chr1:212803520-212803670	HCT-116	colon:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
43	CTCF	chr1:212803423-212803742	GM10266	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
44	MAFK	chr1:212803523-212803708	Hela-S3	cervix:	n/a	chr1:212803672-212803681
45	POLR2A	chr1:212803439-212803963	HL-60	blood:	n/a	n/a
46	CTCF	chr1:212803321-212803699	K562	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
47	CTCF	chr1:212803357-212803746	IMR90	lung:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
48	CTCF	chr1:212803480-212803630	SAEC	small airway:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
49	CTCF	chr1:212803246-212803806	A549	lung:	n/a	chr1:212803562-212803571 chr1:212803584-212803592
50	CTCF	chr1:212803520-212803670	GM12871	blood:	n/a	chr1:212803562-212803571 chr1:212803584-212803592

No.	Distal block	Cell Line	Cell type
1	chr1:212803388..212806406-chr1:212807371..212811389,4	K562	blood:
2	chr1:212650198..212651416-chr1:212803125..212803807,3	MCF-7	breast:
3	chr1:212650175..212651195-chr1:212803104..212804056,5	K562	blood:
4	chr1:212782047..212783624-chr1:212801723..212803752,2	MCF-7	breast:
5	chr1:212646040..212648577-chr1:212802320..212804648,2	K562	blood:
6	chr1:212781459..212784572-chr1:212801208..212804973,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BATF3-2	chr1:212800569-212805905	XLOC_001195
2	lnc-BATF3-2	chr1:212802453-212804805	XLOC_001195
3	lnc-BATF3-2	chr1:212800582-212804801	XLOC_001195

Variant related genes	Relation type
ENSG00000235862	TF binding region
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11571532	1.00[ASN][1000 genomes]
rs11571536	1.00[ASN][1000 genomes]
rs11571538	1.00[ASN][1000 genomes]
rs11571552	1.00[ASN][1000 genomes]
rs17019442	1.00[ASN][1000 genomes]
rs35777725	1.00[ASN][1000 genomes]
rs3890801	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55854080	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023947	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6540751	1.00[ASN][1000 genomes]
rs6656504	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670396	1.00[ASN][1000 genomes]
rs6682816	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756370	1.00[ASN][1000 genomes]
rs72756371	1.00[ASN][1000 genomes]
rs74138599	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138600	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138601	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551520	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212793600-212810600	Weak transcription	Esophagus	oesophagus
2	chr1:212794400-212803600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:212794400-212812200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:212799400-212803600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212800800-212803800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:212801000-212803800	Enhancers	Fetal Heart	heart
7	chr1:212801400-212803600	Enhancers	Fetal Intestine Large	intestine
8	chr1:212801400-212803600	Enhancers	Fetal Intestine Small	intestine
9	chr1:212801400-212803800	Enhancers	Liver	Liver
10	chr1:212801600-212803800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:212802400-212803800	Enhancers	Lung	lung
12	chr1:212802400-212804400	Enhancers	Thymus	Thymus
13	chr1:212802600-212805000	Enhancers	Fetal Thymus	thymus
14	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
15	chr1:212802800-212803600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:212802800-212803600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:212802800-212803600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:212802800-212803800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr1:212802800-212803800	Enhancers	Placenta	Placenta
20	chr1:212802800-212804000	Bivalent Enhancer	HepG2	liver
21	chr1:212803000-212803600	Enhancers	Fetal Muscle Leg	muscle
22	chr1:212803000-212803600	Enhancers	NHDF-Ad	bronchial
23	chr1:212803000-212803800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:212803000-212803800	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:212803000-212803800	Enhancers	Right Ventricle	heart
26	chr1:212803000-212804200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr1:212803000-212804600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:212803000-212805000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:212803200-212803600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:212803200-212803600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:212803200-212803600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:212803200-212803600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:212803200-212803600	Enhancers	Brain Hippocampus Middle	brain
34	chr1:212803200-212803600	Bivalent Enhancer	NHLF	lung
35	chr1:212803200-212803800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:212803200-212803800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:212803200-212803800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:212803200-212803800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:212803200-212803800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
40	chr1:212803200-212803800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr1:212803200-212803800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:212803200-212803800	Enhancers	Brain Anterior Caudate	brain
43	chr1:212803200-212803800	Enhancers	Brain Substantia Nigra	brain
44	chr1:212803200-212803800	Enhancers	Left Ventricle	heart
45	chr1:212803200-212803800	Enhancers	Right Atrium	heart
46	chr1:212803200-212804000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:212803200-212804000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:212803200-212804000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:212803200-212804200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr1:212803200-212804200	Enhancers	Primary B cells from peripheral blood	blood

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