Variant report

Variant	rs62169378
Chromosome Location	chr2:152265561-152265562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr2:152265196-152265776	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr2:152265319-152267211	H1-hESC	embryonic stem cell:	n/a	chr2:152267181-152267190 chr2:152266852-152266863
3	SP1	chr2:152265190-152265757	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr2:152265402-152265595	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr2:152265336-152265669	H1-hESC	embryonic stem cell:	n/a	n/a
6	NR2F2	chr2:152265285-152267404	K562	blood:	n/a	n/a
7	EP300	chr2:152265203-152265689	H1-hESC	embryonic stem cell:	n/a	n/a
8	POU5F1	chr2:152265313-152265710	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr2:152265262-152265660	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr2:152265311-152265608	H1-hESC	embryonic stem cell:	n/a	n/a
11	NANOG	chr2:152265315-152265632	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr2:152265253-152265759	H1-hESC	embryonic stem cell:	n/a	n/a
13	GTF2F1	chr2:152265384-152265588	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUN	chr2:152265511-152267982	K562	blood:	n/a	chr2:152267181-152267190 chr2:152266852-152266863
15	RAD21	chr2:152265206-152265666	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr2:152265360-152265726	H1-hESC	embryonic stem cell:	n/a	n/a
17	CBX3	chr2:152265455-152267418	K562	blood:	n/a	n/a
18	ATF2	chr2:152265349-152265777	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr2:152265357-152265753	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	chr2:152265520-152265570	ECC-1	luminal epithelium:	n/a
2	chr2:152265520-152265570	CMK	blood:	n/a
3	chr2:152265520-152265570	HEK293	kidney:	embryo
4	chr2:152265520-152265570	GM19239	blood:	n/a
5	chr2:152265520-152265570	ProgFib	skin:	n/a
6	chr2:152265520-152265570	GM12878	blood:	n/a
7	chr2:152265520-152265570	NHBE	bronchial:	n/a
8	chr2:152265520-152265570	NB4	blood:	n/a
9	chr2:152265520-152265570	LNCaP	prostate:	n/a
10	chr2:152265520-152265570	SK-N-SH_RA	brain:	n/a
11	chr2:152265520-152265570	GM06990	blood:	n/a
12	chr2:152265520-152265570	BE2_C	brain:	n/a
13	chr2:152265520-152265570	RPTEC	kidney:	n/a
14	chr2:152265520-152265570	K562	blood:	n/a
15	chr2:152265520-152265570	HCM	heart:	n/a
16	chr2:152265520-152265570	ovcar-3	ovarian:	n/a
17	chr2:152265520-152265570	MCF-7	breast:	n/a
18	chr2:152265520-152265570	SK-N-SH	brain:	n/a
19	chr2:152265520-152265570	H1-hESC	embryonic stem cell:	embryo
20	chr2:152265520-152265570	HRPEpiC	eye:	n/a
21	chr2:152265520-152265570	AG04449	skin:	fetal
22	chr2:152265520-152265570	Hepatocyte	liver:	n/a
23	chr2:152265520-152265570	Caco-2	colon:	n/a
24	chr2:152265520-152265570	HRE	kidney:	n/a
25	chr2:152265520-152265570	GM12891	blood:	n/a
26	chr2:152265520-152265570	NHDF-neo	bronchial:	n/a
27	chr2:152265520-152265570	Jurkat	blood:	n/a
28	chr2:152265520-152265570	HCT-116	colon:	n/a
29	chr2:152265520-152265570	HepG2	liver:	n/a
30	chr2:152265520-152265570	T-47D	breast:	n/a
31	chr2:152265520-152265570	AG04450	lung:	fetal
32	chr2:152265520-152265570	HUVEC	blood vessel:	n/a
33	chr2:152265520-152265570	A549	lung:	n/a
34	chr2:152265520-152265570	U87	brain:	n/a
35	chr2:152265520-152265570	HAEpiC	amniotic membrane:	n/a
36	chr2:152265520-152265570	HRCEpiC	kidney:	n/a
37	chr2:152265520-152265570	SKMC	muscle:	n/a
38	chr2:152265520-152265570	HMEC	breast:	n/a
39	chr2:152265520-152265570	PrEC	prostate:	n/a
40	chr2:152265520-152265570	PANC-1	pancreas:	n/a
41	chr2:152265520-152265570	AG09319	gingival:	n/a
42	chr2:152265520-152265570	AoSMC	blood vessel:	n/a
43	chr2:152265520-152265570	Hela-S3	cervix:	n/a
44	chr2:152265520-152265570	HEEpiC	esophagus:	n/a
45	chr2:152265520-152265570	NT2-D1	testis:	n/a
46	chr2:152265520-152265570	SK-N-MC	brain:	n/a
47	chr2:152265520-152265570	PFSK-1	brain:	n/a
48	chr2:152265520-152265570	HL-60	blood:	n/a
49	chr2:152265520-152265570	HCF	heart:	n/a
50	chr2:152265520-152265570	AG10803	skin:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152144813..152149803-chr2:152261382..152268379,11	K562	blood:
2	chr2:152262551..152270893-chr2:152273971..152280003,13	K562	blood:
3	chr2:152145011..152148288-chr2:152265460..152267609,4	MCF-7	breast:
4	chr2:152116678..152120470-chr2:152265032..152268454,8	MCF-7	breast:
5	chr2:152146157..152147960-chr2:152264680..152266212,2	K562	blood:
6	chr2:152116022..152119511-chr2:152263980..152267786,5	K562	blood:
7	chr2:152144798..152147073-chr2:152265350..152268359,5	MCF-7	breast:
8	chr2:152258517..152261136-chr2:152264603..152266295,2	K562	blood:

No data

Variant related genes	Relation type
RIF1	TF binding region
RIF1	CpG island
ENSG00000080345	Chromatin interaction
ENSG00000184898	Chromatin interaction
ENSG00000123609	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11896481	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16830019	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830036	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16830047	0.85[ASN][1000 genomes]
rs16830059	0.84[ASN][1000 genomes]
rs16830061	0.86[ASN][1000 genomes]
rs16830067	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16830086	0.86[ASN][1000 genomes]
rs16830090	0.84[ASN][1000 genomes]
rs16830096	0.84[ASN][1000 genomes]
rs16830159	0.80[ASN][1000 genomes]
rs1993206	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732308	0.82[ASN][1000 genomes]
rs4468813	0.86[ASN][1000 genomes]
rs4491723	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4494741	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55654831	0.92[ASN][1000 genomes]
rs55900984	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56898485	0.86[ASN][1000 genomes]
rs62169373	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62169374	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62169380	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62169382	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62169384	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62169385	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169386	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6726640	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6733645	0.86[ASN][1000 genomes]
rs6742953	0.86[ASN][1000 genomes]
rs72860229	0.95[ASN][1000 genomes]
rs72860230	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72860235	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72860236	0.91[ASN][1000 genomes]
rs7422009	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7593710	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598855	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152261600-152266000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:152261800-152265800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:152264000-152265600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:152264800-152268000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:152265000-152268600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:152265200-152265800	Enhancers	K562	blood
7	chr2:152265200-152266000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:152265200-152266000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:152265200-152266200	Weak transcription	Right Atrium	heart
10	chr2:152265400-152265600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:152265400-152265800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:152265400-152266000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:152265400-152266000	Enhancers	Hela-S3	cervix
14	chr2:152265400-152266200	Enhancers	Placenta	Placenta
15	chr2:152265400-152267800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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