Variant report

Variant	rs62398706
Chromosome Location	chr6:31047662-31047663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:198)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:198 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31047660-31047810	HRE	kidney:	n/a	n/a
2	RAD21	chr6:31047526-31047845	GM12878	blood:	n/a	n/a
3	CTCF	chr6:31047660-31047810	A549	lung:	n/a	n/a
4	CTCF	chr6:31047615-31047899	Medullo	brain:	n/a	n/a
5	CHD2	chr6:31047454-31047785	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr6:31047532-31047939	K562	blood:	n/a	n/a
7	RAD21	chr6:31047351-31048074	HCT-116	colon:	n/a	n/a
8	CUX1	chr6:31047660-31047986	K562	blood:	n/a	n/a
9	RAD21	chr6:31047532-31047923	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr6:31047660-31047810	AoAF	blood vessel:	n/a	n/a
11	RAD21	chr6:31047526-31047926	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr6:31047620-31047770	HUVEC	blood vessel:	n/a	n/a
13	RAD21	chr6:31047517-31048083	MCF-7	breast:	n/a	n/a
14	CTCF	chr6:31047660-31047810	AG09319	gingival:	n/a	n/a
15	CTCF	chr6:31047652-31047853	GM13976	blood:	n/a	n/a
16	RAD21	chr6:31047558-31047901	A549	lung:	n/a	n/a
17	CTCF	chr6:31047644-31047883	Kidney_OC	kidney:	n/a	n/a
18	CTCF	chr6:31047660-31047810	HMF	breast:	n/a	n/a
19	CTCF	chr6:31047620-31047770	A549	lung:	n/a	n/a
20	TCF7L2	chr6:31047450-31047861	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr6:31047494-31047893	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr6:31047463-31047964	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr6:31047660-31047810	BJ	skin:	n/a	n/a
24	CTCF	chr6:31047620-31047770	GM12866	blood:	n/a	n/a
25	CTCF	chr6:31047630-31047822	SK-N-SH_RA	brain:	n/a	n/a
26	TBL1XR1	chr6:31047637-31047821	K562	blood:	n/a	n/a
27	CTCF	chr6:31047319-31048175	SK-N-SH	brain:	n/a	n/a
28	RAD21	chr6:31047528-31047920	ECC-1	luminal epithelium:	n/a	n/a
29	CTCF	chr6:31047536-31047964	K562	blood:	n/a	n/a
30	CTCF	chr6:31047377-31048084	HCT-116	colon:	n/a	n/a
31	BCLAF1	chr6:31047470-31047930	GM12878	blood:	n/a	n/a
32	CTCF	chr6:31047660-31047810	HEK293	kidney:	n/a	n/a
33	CTCF	chr6:31047660-31047810	HAc	cerebellar:	n/a	n/a
34	CTCF	chr6:31047476-31047966	HepG2	liver:	n/a	n/a
35	CTCF	chr6:31047660-31047810	GM12865	blood:	n/a	n/a
36	CTCF	chr6:31047577-31047865	H1-hESC	embryonic stem cell:	n/a	n/a
37	GATA3	chr6:31047606-31047908	T-47D	breast:	n/a	n/a
38	CTCF	chr6:31047660-31047810	GM12868	blood:	n/a	n/a
39	CTCF	chr6:31047660-31047810	GM12871	blood:	n/a	n/a
40	CTCF	chr6:31047639-31047865	Hela-S3	cervix:	n/a	n/a
41	ELF1	chr6:31047443-31047887	K562	blood:	n/a	n/a
42	CTCF	chr6:31047338-31047980	HCT-116	colon:	n/a	n/a
43	CTCF	chr6:31047640-31047790	BE2_C	brain:	n/a	n/a
44	MYC	chr6:31047588-31047773	MCF10A-Er-Src	breast:	n/a	n/a
45	CTCF	chr6:31047605-31047874	GM10266	blood:	n/a	n/a
46	TCF7L2	chr6:31047543-31047846	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr6:31047507-31047883	K562	blood:	n/a	n/a
48	GATA2	chr6:31047477-31047892	SH-SY5Y	brain:	n/a	n/a
49	CEBPD	chr6:31047594-31047976	K562	blood:	n/a	n/a
50	ZNF143	chr6:31047508-31047873	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31047653-31047703	HRCEpiC	kidney:	n/a
2	chr6:31047653-31047703	HCM	heart:	n/a
3	chr6:31047653-31047703	K562	blood:	n/a
4	chr6:31047653-31047703	HIPEpiC	eye:	n/a
5	chr6:31047653-31047703	NH-A	brain:	n/a
6	chr6:31047653-31047703	GM12878	blood:	n/a
7	chr6:31047653-31047703	U87	brain:	n/a
8	chr6:31047653-31047703	HEK293	kidney:	embryo
9	chr6:31047653-31047703	LNCaP	prostate:	n/a
10	chr6:31047653-31047703	AoSMC	blood vessel:	n/a
11	chr6:31047653-31047703	RPTEC	kidney:	n/a
12	chr6:31047653-31047703	HCT-116	colon:	n/a
13	chr6:31047653-31047703	MCF-7	breast:	n/a
14	chr6:31047653-31047703	NB4	blood:	n/a
15	chr6:31047653-31047703	SK-N-SH	brain:	n/a
16	chr6:31047653-31047703	HAEpiC	amniotic membrane:	n/a
17	chr6:31047653-31047703	HCPEpiC	choroid plexus:	n/a
18	chr6:31047653-31047703	AG09319	gingival:	n/a
19	chr6:31047653-31047703	BE2_C	brain:	n/a
20	chr6:31047653-31047703	AG04449	skin:	fetal
21	chr6:31047653-31047703	AG10803	skin:	n/a
22	chr6:31047653-31047703	HRPEpiC	eye:	n/a
23	chr6:31047653-31047703	Hela-S3	cervix:	n/a
24	chr6:31047653-31047703	SK-N-MC	brain:	n/a
25	chr6:31047653-31047703	HUVEC	blood vessel:	n/a
26	chr6:31047653-31047703	PrEC	prostate:	n/a
27	chr6:31047653-31047703	GM12891	blood:	n/a
28	chr6:31047653-31047703	IMR90	lung:	fetal
29	chr6:31047653-31047703	GM19239	blood:	n/a
30	chr6:31047653-31047703	HepG2	liver:	n/a
31	chr6:31047653-31047703	HCF	heart:	n/a
32	chr6:31047653-31047703	HNPCEpiC	eye:	n/a
33	chr6:31047653-31047703	AG09309	skin:	n/a
34	chr6:31047653-31047703	NHDF-neo	bronchial:	n/a
35	chr6:31047653-31047703	SK-N-SH_RA	brain:	n/a
36	chr6:31047653-31047703	PANC-1	pancreas:	n/a
37	chr6:31047653-31047703	SKMC	muscle:	n/a
38	chr6:31047653-31047703	GM12892	blood:	n/a
39	chr6:31047653-31047703	NT2-D1	testis:	n/a
40	chr6:31047653-31047703	Hepatocyte	liver:	n/a
41	chr6:31047653-31047703	H1-hESC	embryonic stem cell:	embryo
42	chr6:31047653-31047703	ECC-1	luminal epithelium:	n/a
43	chr6:31047653-31047703	Caco-2	colon:	n/a
44	chr6:31047653-31047703	HEEpiC	esophagus:	n/a
45	chr6:31047653-31047703	AG04450	lung:	fetal
46	chr6:31047653-31047703	Jurkat	blood:	n/a
47	chr6:31047653-31047703	PFSK-1	brain:	n/a
48	chr6:31047653-31047703	T-47D	breast:	n/a
49	chr6:31047653-31047703	HMEC	breast:	n/a
50	chr6:31047653-31047703	HPAEpiC	pulmonary alveolar:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30706873..30708855-chr6:31047414..31049286,2	MCF-7	breast:
2	chr6:30881800..30882463-chr6:31047201..31048108,3	K562	blood:
3	chr6:30882935..30883738-chr6:31047207..31048204,5	MCF-7	breast:
4	chr6:30890243..30892584-chr6:31046594..31049304,2	K562	blood:
5	chr6:31025808..31026599-chr6:31047303..31047806,2	MCF-7	breast:
6	chr6:30880536..30882349-chr6:31046191..31049160,2	MCF-7	breast:
7	chr6:30796035..30796933-chr6:31047284..31048260,5	K562	blood:
8	chr6:30705562..30707889-chr6:31046785..31048860,2	K562	blood:
9	chr6:30646469..30647409-chr6:31047261..31047791,2	K562	blood:
10	chr6:31046659..31048229-chr6:31054685..31056795,2	K562	blood:
11	chr6:30711725..30712585-chr6:31047248..31048213,2	K562	blood:
12	chr6:30794295..30796763-chr6:31046294..31048518,2	K562	blood:
13	chr6:30795553..30798547-chr6:31047282..31049904,2	MCF-7	breast:
14	chr6:31025998..31026666-chr6:31047275..31048136,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-1133P	TF binding region
RNU6-1133P	CpG island
ENSG00000137411	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044870	0.86[ASN][1000 genomes]
rs11756674	0.85[EUR][1000 genomes]
rs11756797	1.00[EUR][1000 genomes]
rs11758495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130077	0.86[ASN][1000 genomes]
rs2233945	0.86[ASN][1000 genomes]
rs2233946	0.86[ASN][1000 genomes]
rs2233947	0.93[ASN][1000 genomes]
rs28742577	0.86[ASN][1000 genomes]
rs35157432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62398740	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62398741	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62398744	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62399060	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62399061	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62399064	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62399065	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62399066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62400570	0.93[ASN][1000 genomes]
rs62401701	0.83[EUR][1000 genomes]
rs9263733	0.93[ASN][1000 genomes]
rs9263745	0.86[ASN][1000 genomes]
rs9263766	0.86[ASN][1000 genomes]
rs9263768	0.86[ASN][1000 genomes]
rs9263769	0.83[ASN][1000 genomes]
rs9263774	0.86[ASN][1000 genomes]
rs9263775	0.86[ASN][1000 genomes]
rs9263776	0.86[ASN][1000 genomes]
rs9263777	0.86[ASN][1000 genomes]
rs9263778	0.86[ASN][1000 genomes]
rs9263781	0.86[ASN][1000 genomes]
rs9263782	0.86[ASN][1000 genomes]
rs9263783	0.86[ASN][1000 genomes]
rs9263785	0.86[ASN][1000 genomes]
rs9263786	0.86[ASN][1000 genomes]
rs9263790	0.86[ASN][1000 genomes]
rs9263792	0.86[ASN][1000 genomes]
rs9263794	0.83[ASN][1000 genomes]
rs9263796	0.86[ASN][1000 genomes]
rs9263822	0.86[ASN][1000 genomes]
rs9263832	0.86[ASN][1000 genomes]
rs9263843	0.86[ASN][1000 genomes]
rs9263855	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
10	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
11	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
12	nsv884134	chr6:31028345-31048263	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:31039000-31048200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:31040600-31055000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:31040600-31062400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:31041600-31053200	Weak transcription	NH-A	brain
6	chr6:31043200-31051200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:31044600-31049800	Weak transcription	HSMMtube	muscle
8	chr6:31046600-31053400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:31047000-31048200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:31047200-31047800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:31047200-31047800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:31047200-31047800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:31047200-31047800	Enhancers	Fetal Thymus	thymus
14	chr6:31047200-31048000	Enhancers	Primary T cells from cord blood	blood
15	chr6:31047200-31048000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:31047200-31048000	Enhancers	Dnd41	blood
17	chr6:31047400-31047800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:31047400-31047800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:31047400-31047800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:31047400-31047800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:31047400-31047800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:31047400-31047800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr6:31047400-31047800	Enhancers	Primary B cells from cord blood	blood
24	chr6:31047400-31047800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr6:31047400-31047800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:31047400-31047800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:31047400-31047800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:31047400-31047800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:31047400-31047800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:31047400-31047800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:31047400-31047800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:31047400-31047800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:31047400-31047800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:31047400-31047800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:31047400-31047800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:31047400-31047800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:31047400-31047800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:31047400-31047800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:31047400-31047800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:31047400-31047800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr6:31047400-31047800	Enhancers	Liver	Liver
42	chr6:31047400-31047800	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr6:31047400-31047800	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr6:31047400-31047800	Enhancers	Colonic Mucosa	Colon
45	chr6:31047400-31047800	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:31047400-31047800	Flanking Active TSS	Fetal Brain Female	brain
47	chr6:31047400-31047800	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr6:31047400-31047800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
49	chr6:31047400-31047800	Active TSS	Ovary	ovary
50	chr6:31047400-31047800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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