Variant report

Variant	rs62420323
Chromosome Location	chr6:71122553-71122554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:171)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:171 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr6:71122546-71123757	HepG2	liver:	n/a	n/a
2	MAX	chr6:71122434-71122977	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:71122516-71123483	ECC-1	luminal epithelium:	n/a	n/a
4	POU2F2	chr6:71122501-71123041	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:71122296-71124175	SK-N-MC	brain:	n/a	n/a
6	ATF1	chr6:71122490-71123310	K562	blood:	n/a	n/a
7	IRF3	chr6:71122429-71122568	GM12878	blood:	n/a	n/a
8	ATF2	chr6:71122536-71123169	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr6:71122509-71123388	K562	blood:	n/a	n/a
10	MAX	chr6:71122487-71124119	A549	lung:	n/a	chr6:71123792-71123808 chr6:71123800-71123811 chr6:71123796-71123815 chr6:71123801-71123811 chr6:71123092-71123102
11	POLR2A	chr6:71122120-71124084	K562	blood:	n/a	n/a
12	E2F6	chr6:71122427-71124217	K562	blood:	n/a	chr6:71122913-71122920 chr6:71123793-71123802 chr6:71122908-71122922 chr6:71122937-71122951 chr6:71122936-71122951
13	POLR2A	chr6:71122499-71124106	GM18505	blood:	n/a	n/a
14	POLR2A	chr6:71122488-71123356	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:71122317-71124183	GM19099	blood:	n/a	n/a
16	TAF1	chr6:71122553-71123366	K562	blood:	n/a	n/a
17	POLR2A	chr6:71121858-71124306	GM12878	blood:	n/a	n/a
18	SIN3A	chr6:71122392-71124181	H1-hESC	embryonic stem cell:	n/a	chr6:71123005-71123014
19	POLR2A	chr6:71122070-71123458	MCF10A-Er-Src	breast:	n/a	n/a
20	RCOR1	chr6:71122396-71123373	K562	blood:	n/a	n/a
21	POLR2A	chr6:71122511-71124048	NB4	blood:	n/a	n/a
22	POLR2A	chr6:71122458-71123456	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:71122448-71123654	K562	blood:	n/a	n/a
24	HCFC1	chr6:71122330-71123489	K562	blood:	n/a	n/a
25	CEBPB	chr6:71122137-71122621	A549	lung:	n/a	chr6:71122349-71122360
26	POLR2A	chr6:71122480-71123390	GM12892	blood:	n/a	n/a
27	BCLAF1	chr6:71122461-71123071	GM12878	blood:	n/a	n/a
28	MAX	chr6:71122519-71123433	ECC-1	luminal epithelium:	n/a	chr6:71123092-71123102
29	TAF1	chr6:71122527-71123415	K562	blood:	n/a	n/a
30	POLR2A	chr6:71122435-71124163	Raji	blood:	n/a	n/a
31	TCF12	chr6:71122540-71123313	ECC-1	luminal epithelium:	n/a	n/a
32	GATA2	chr6:71122472-71123505	SH-SY5Y	brain:	n/a	chr6:71122477-71122484 chr6:71122475-71122484
33	FOXM1	chr6:71122481-71123614	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:71122504-71123406	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr6:71122514-71123139	GM12891	blood:	n/a	n/a
36	JUND	chr6:71122479-71123495	K562	blood:	n/a	n/a
37	POLR2A	chr6:71122553-71123400	U87	brain:	n/a	n/a
38	POLR2A	chr6:71122542-71124150	GM12878	blood:	n/a	n/a
39	ZBTB33	chr6:71122408-71123354	SK-N-SH	brain:	n/a	chr6:71122942-71122952 chr6:71122939-71122954
40	GATA3	chr6:71122520-71123344	A549	lung:	n/a	n/a
41	TBP	chr6:71122409-71124050	H1-hESC	embryonic stem cell:	n/a	n/a
42	JUND	chr6:71122476-71123448	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:71122538-71123820	GM12878	blood:	n/a	n/a
44	CHD2	chr6:71122428-71123407	HepG2	liver:	n/a	chr6:71122913-71122920 chr6:71123094-71123104
45	POLR2A	chr6:71121804-71123819	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:71122529-71123536	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr6:71122348-71123952	GM19193	blood:	n/a	n/a
48	POLR2A	chr6:71119930-71123467	K562	blood:	n/a	n/a
49	HCFC1	chr6:71122176-71123572	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr6:71122233-71123426	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:71122524-71122574	HCT-116	colon:	n/a
2	chr6:71122524-71122574	SK-N-MC	brain:	n/a
3	chr6:71122524-71122574	HAEpiC	amniotic membrane:	n/a
4	chr6:71122524-71122574	HCM	heart:	n/a
5	chr6:71122524-71122574	PANC-1	pancreas:	n/a
6	chr6:71122524-71122574	HCF	heart:	n/a
7	chr6:71122524-71122574	LNCaP	prostate:	n/a
8	chr6:71122524-71122574	NHDF-neo	bronchial:	n/a
9	chr6:71122524-71122574	HEEpiC	esophagus:	n/a
10	chr6:71122524-71122574	NHBE	bronchial:	n/a
11	chr6:71122524-71122574	GM19239	blood:	n/a
12	chr6:71122524-71122574	HEK293	kidney:	embryo
13	chr6:71122524-71122574	K562	blood:	n/a
14	chr6:71122524-71122574	AoSMC	blood vessel:	n/a
15	chr6:71122524-71122574	PFSK-1	brain:	n/a
16	chr6:71122524-71122574	Hepatocyte	liver:	n/a
17	chr6:71122524-71122574	A549	lung:	n/a
18	chr6:71122524-71122574	ECC-1	luminal epithelium:	n/a
19	chr6:71122524-71122574	AG09309	skin:	n/a
20	chr6:71122524-71122574	SKMC	muscle:	n/a
21	chr6:71122524-71122574	NT2-D1	testis:	n/a
22	chr6:71122524-71122574	GM12892	blood:	n/a
23	chr6:71122524-71122574	HL-60	blood:	n/a
24	chr6:71122524-71122574	AG09319	gingival:	n/a
25	chr6:71122524-71122574	HUVEC	blood vessel:	n/a
26	chr6:71122524-71122574	MCF10A-Er-Src	breast:	n/a
27	chr6:71122524-71122574	HRPEpiC	eye:	n/a
28	chr6:71122524-71122574	AG10803	skin:	n/a
29	chr6:71122524-71122574	U87	brain:	n/a
30	chr6:71122524-71122574	AG04449	skin:	fetal
31	chr6:71122524-71122574	HIPEpiC	eye:	n/a
32	chr6:71122524-71122574	SK-N-SH_RA	brain:	n/a
33	chr6:71122524-71122574	SAEC	small airway:	n/a
34	chr6:71122524-71122574	RPTEC	kidney:	n/a
35	chr6:71122524-71122574	HMEC	breast:	n/a
36	chr6:71122524-71122574	NB4	blood:	n/a
37	chr6:71122524-71122574	T-47D	breast:	n/a
38	chr6:71122524-71122574	BJ	skin:	n/a
39	chr6:71122524-71122574	BE2_C	brain:	n/a
40	chr6:71122524-71122574	Hela-S3	cervix:	n/a
41	chr6:71122524-71122574	Caco-2	colon:	n/a
42	chr6:71122524-71122574	GM06990	blood:	n/a
43	chr6:71122524-71122574	HepG2	liver:	n/a
44	chr6:71122524-71122574	Jurkat	blood:	n/a
45	chr6:71122524-71122574	NH-A	brain:	n/a
46	chr6:71122524-71122574	IMR90	lung:	fetal
47	chr6:71122524-71122574	HCPEpiC	choroid plexus:	n/a
48	chr6:71122524-71122574	CMK	blood:	n/a
49	chr6:71122524-71122574	AG04450	lung:	fetal
50	chr6:71122524-71122574	HNPCEpiC	eye:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:16186106..16187092-chr6:71122372..71122959,2	Hela-S3	cervix:
2	chr6:71121490..71124764-chr6:71274758..71276919,3	K562	blood:
3	chr12:1058193..1058819-chr6:71122547..71123405,2	HCT-116	colon:
4	chr19:49468459..49469034-chr6:71122515..71123021,2	NB4	blood:
5	chr1:144533691..144534509-chr6:71122358..71122907,2	HCT-116	colon:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL9A1-1	chr6:71122531-71122765	ENSG00000224349.2

No data

Variant related genes	Relation type
FAM135A	TF binding region
FAM135A	CpG island
ENSG00000201699	Chromatin interaction
ENSG00000087086	Chromatin interaction
ENSG00000002016	Chromatin interaction
ENSG00000167460	Chromatin interaction
ENSG00000154079	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13194594	0.84[EUR][1000 genomes]
rs13197182	0.82[EUR][1000 genomes]
rs13198944	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207234	0.83[EUR][1000 genomes]
rs13210191	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218183	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17634619	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34238069	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34257638	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34798144	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35371002	0.84[EUR][1000 genomes]
rs35426375	0.82[EUR][1000 genomes]
rs35457911	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35462174	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62420317	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62420326	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421868	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421869	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62421874	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62421877	0.83[EUR][1000 genomes]
rs997350	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1026229	chr6:71016272-71183503	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv886144	chr6:71018467-71214201	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1032876	chr6:71048428-71145166	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1027161	chr6:71106657-71145166	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71121400-71125200	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:71121600-71122800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr6:71121800-71124400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:71121800-71124600	Active TSS	Fetal Kidney	kidney
5	chr6:71121800-71124800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:71122000-71122600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr6:71122000-71122600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:71122000-71122600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:71122000-71122600	Weak transcription	Gastric	stomach
10	chr6:71122000-71122800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:71122000-71122800	Flanking Active TSS	HUVEC	blood vessel
12	chr6:71122000-71123800	Active TSS	Muscle Satellite Cultured Cells	--
13	chr6:71122000-71124000	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr6:71122000-71124000	Active TSS	Hela-S3	cervix
15	chr6:71122000-71124000	Active TSS	NHLF	lung
16	chr6:71122000-71124200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:71122000-71124400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:71122000-71124400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:71122000-71124400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:71122000-71124400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:71122000-71124600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:71122000-71124600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:71122000-71124600	Active TSS	Colonic Mucosa	Colon
24	chr6:71122000-71124600	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:71122000-71124800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:71122000-71124800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:71122000-71125000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:71122000-71125200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:71122000-71126200	Active TSS	GM12878-XiMat	blood
30	chr6:71122200-71122600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:71122200-71122600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:71122200-71122600	Flanking Active TSS	Liver	Liver
33	chr6:71122200-71122600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr6:71122200-71122600	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr6:71122200-71122600	Flanking Active TSS	Fetal Lung	lung
36	chr6:71122200-71122600	Flanking Active TSS	NHEK	skin
37	chr6:71122200-71122600	Flanking Active TSS	Osteobl	bone
38	chr6:71122200-71122800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:71122200-71122800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:71122200-71122800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:71122200-71123000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:71122200-71123000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:71122200-71123800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:71122200-71123800	Active TSS	Fetal Muscle Leg	muscle
45	chr6:71122200-71124000	Active TSS	NHDF-Ad	bronchial
46	chr6:71122200-71124200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr6:71122200-71124200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:71122200-71124200	Active TSS	Colon Smooth Muscle	Colon
49	chr6:71122200-71124200	Active TSS	Fetal Brain Male	brain
50	chr6:71122200-71124200	Active TSS	HSMMtube	muscle

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