Variant report

Variant	rs2165461
Chromosome Location	chr15:57210627-57210628
allele	C/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	POLR2A	chr15:57210274-57211138	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:57209696-57212423	H1-hESC	embryonic stem cell:	n/a	n/a
3	HNF4A	chr15:57210599-57211003	HepG2	liver:	n/a	n/a
4	ZNF143	chr15:57210418-57211107	K562	blood:	n/a	chr15:57210720-57210738
5	CTCF	chr15:57210390-57210681	MCF-7	breast:	n/a	n/a
6	TAL1	chr15:57210485-57211084	K562	blood:	n/a	n/a
7	ZNF143	chr15:57210156-57211267	GM12878	blood:	n/a	chr15:57210720-57210738
8	POLR2A	chr15:57210182-57212319	GM19099	blood:	n/a	n/a
9	SMC3	chr15:57210522-57210968	K562	blood:	n/a	n/a
10	POLR2A	chr15:57210214-57211868	GM12891	blood:	n/a	n/a
11	CTCF	chr15:57210398-57210658	MCF-7	breast:	n/a	n/a
12	EP300	chr15:57210548-57210999	SK-N-SH_RA	brain:	n/a	chr15:57210924-57210940
13	MAX	chr15:57209841-57210747	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr15:57210120-57211157	ECC-1	luminal epithelium:	n/a	chr15:57210744-57210754
15	PAX5	chr15:57210293-57211039	GM12892	blood:	n/a	n/a
16	POLR2A	chr15:57209256-57213061	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr15:57210480-57210630	WI-38	lung:	n/a	n/a
18	HEY1	chr15:57210478-57211142	HepG2	liver:	n/a	chr15:57210700-57210715
19	POLR2A	chr15:57210558-57211191	Hela-S3	cervix:	n/a	n/a
20	TAF1	chr15:57210021-57212293	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr15:57210377-57211283	Gliobla	brain:	n/a	n/a
22	EGR1	chr15:57210571-57210988	ECC-1	luminal epithelium:	n/a	chr15:57210744-57210757 chr15:57210741-57210755 chr15:57210744-57210757
23	YY1	chr15:57210210-57211198	ECC-1	luminal epithelium:	n/a	chr15:57210743-57210752
24	USF1	chr15:57210451-57211079	ECC-1	luminal epithelium:	n/a	n/a
25	PML	chr15:57210609-57211116	K562	blood:	n/a	n/a
26	CTCF	chr15:57210433-57210633	MCF-7	breast:	n/a	n/a
27	TAF1	chr15:57210291-57211794	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr15:57210381-57211043	U87	brain:	n/a	n/a
29	GATA1	chr15:57210272-57211359	PBDE	blood:	n/a	n/a
30	CTCF	chr15:57210377-57210668	GM10266	blood:	n/a	n/a
31	RELA	chr15:57210327-57210979	GM19193	blood:	n/a	n/a
32	TEAD4	chr15:57210569-57211037	H1-hESC	embryonic stem cell:	n/a	n/a
33	JUN	chr15:57209836-57213020	K562	blood:	n/a	chr15:57211660-57211671 chr15:57211663-57211673 chr15:57212474-57212482 chr15:57211663-57211673 chr15:57212472-57212484 chr15:57211663-57211673 chr15:57212473-57212483
34	MAX	chr15:57209944-57211084	K562	blood:	n/a	chr15:57210744-57210754
35	EP300	chr15:57210567-57210996	H1-hESC	embryonic stem cell:	n/a	chr15:57210924-57210940
36	YY1	chr15:57210351-57211160	SK-N-SH	brain:	n/a	chr15:57210743-57210752
37	CTCF	chr15:57210389-57210680	Fibrobl	skin:	n/a	n/a
38	POLR2A	chr15:57210231-57211221	A549	lung:	n/a	n/a
39	MYC	chr15:57209765-57211087	K562	blood:	n/a	chr15:57210744-57210754
40	MAZ	chr15:57210136-57211848	GM12878	blood:	n/a	chr15:57210744-57210754
41	EP300	chr15:57210261-57211203	ECC-1	luminal epithelium:	n/a	chr15:57210924-57210940
42	E2F6	chr15:57209826-57211149	H1-hESC	embryonic stem cell:	n/a	chr15:57210776-57210785 chr15:57210743-57210752 chr15:57211095-57211105 chr15:57210740-57210752
43	MAZ	chr15:57210239-57212203	Hela-S3	cervix:	n/a	chr15:57210744-57210754
44	CTCF	chr15:57210500-57210650	BE2_C	brain:	n/a	n/a
45	YY1	chr15:57210618-57211010	A549	lung:	n/a	chr15:57210743-57210752
46	SP1	chr15:57210515-57210963	K562	blood:	n/a	chr15:57210741-57210753 chr15:57210742-57210751 chr15:57210743-57210752 chr15:57210741-57210753 chr15:57210742-57210751 chr15:57210742-57210756 chr15:57210925-57210934
47	CREB1	chr15:57210393-57211125	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr15:57210281-57211200	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr15:57210519-57211256	HepG2	liver:	n/a	n/a
50	POLR2A	chr15:57210409-57212360	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57023339..57026885-chr15:57210242..57212303,3	MCF-7	breast:
2	chr15:57024542..57026335-chr15:57210196..57212175,2	K562	blood:
3	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:
4	chr13:111213805..111214409-chr15:57210301..57210849,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-3	chr15:57209738-57210697	ENSG00000248500
2	lnc-MNS1-3	chr15:57209738-57210691	ENSG00000259484.1

Variant related genes	Relation type
ZNF280D	TF binding region
TCF12	TF binding region
ENSG00000139832	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11630195	0.80[ASN][1000 genomes]
rs11631228	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11631732	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632592	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858471	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12899187	0.81[AMR][1000 genomes]
rs12900986	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12901780	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12904784	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906873	0.80[ASN][1000 genomes]
rs12906936	0.80[ASN][1000 genomes]
rs12908670	0.85[ASN][1000 genomes]
rs12914625	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12916237	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12916958	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17819700	0.80[ASN][1000 genomes]
rs2053472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111891	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2116065	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2116066	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs213164	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414490	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2583108	0.86[ASN][1000 genomes]
rs2585082	0.83[ASN][1000 genomes]
rs34262415	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35646942	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3803454	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3803455	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4399497	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774898	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774899	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774902	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62022986	0.81[AMR][1000 genomes]
rs62025331	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs715338	0.81[EUR][1000 genomes];0.94[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv3419108	chr15:57209560-57212908	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
8	esv3345364	chr15:57210185-57213033	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57209200-57212200	Active TSS	Stomach Smooth Muscle	stomach
2	chr15:57209200-57213000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:57209200-57213000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:57209400-57211000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:57209400-57212200	Active TSS	Colon Smooth Muscle	Colon
6	chr15:57209400-57212800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:57209400-57213200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:57209400-57213400	Active TSS	HSMMtube	muscle
9	chr15:57209400-57217200	Active TSS	Thymus	Thymus
10	chr15:57209600-57210800	Flanking Active TSS	Dnd41	blood
11	chr15:57209600-57212600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:57209600-57212800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:57209600-57212800	Active TSS	Ovary	ovary
14	chr15:57209600-57212800	Active TSS	Right Ventricle	heart
15	chr15:57209600-57213400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr15:57209800-57212400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr15:57209800-57212400	Active TSS	Esophagus	oesophagus
18	chr15:57209800-57212600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:57209800-57212600	Active TSS	Aorta	Aorta
20	chr15:57209800-57212800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:57209800-57213200	Active TSS	Brain Cingulate Gyrus	brain
22	chr15:57209800-57213200	Active TSS	Fetal Kidney	kidney
23	chr15:57210000-57212000	Active TSS	Fetal Lung	lung
24	chr15:57210000-57212200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
25	chr15:57210000-57212200	Active TSS	Fetal Brain Female	brain
26	chr15:57210000-57212400	Active TSS	Brain Angular Gyrus	brain
27	chr15:57210000-57212400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:57210000-57212400	Active TSS	Lung	lung
29	chr15:57210000-57212400	Active TSS	Placenta Amnion	Placenta Amnion
30	chr15:57210000-57212400	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:57210000-57212400	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr15:57210000-57212400	Active TSS	Hela-S3	cervix
33	chr15:57210000-57212600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:57210000-57212600	Active TSS	Brain Anterior Caudate	brain
35	chr15:57210000-57212600	Active TSS	A549	lung
36	chr15:57210000-57212600	Active TSS	HSMM	muscle
37	chr15:57210000-57212800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr15:57210000-57212800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr15:57210000-57212800	Active TSS	Fetal Intestine Large	intestine
40	chr15:57210000-57212800	Active TSS	Psoas Muscle	Psoas
41	chr15:57210000-57213000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:57210000-57213200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:57210000-57213400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:57210200-57210800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:57210200-57212000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr15:57210200-57212000	Active TSS	Liver	Liver
47	chr15:57210200-57212000	Active TSS	Duodenum Mucosa	Duodenum
48	chr15:57210200-57212000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr15:57210200-57212200	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr15:57210200-57212200	Active TSS	Primary T helper cells PMA-I stimulated	--

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