Variant report

Variant	rs59295315
Chromosome Location	chr12:56708576-56708577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56708568-56711261	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:56708516-56710469	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:56708555-56708712	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:56708561-56708981	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:56708544-56710536	GM12878	blood:	n/a	n/a
6	MXI1	chr12:56708359-56710640	IMR90	lung:	n/a	chr12:56709964-56709973
7	CTCF	chr12:56708560-56708710	GM12871	blood:	n/a	n/a
8	POLR2A	chr12:56708560-56710671	K562	blood:	n/a	n/a
9	POLR2A	chr12:56708399-56710457	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:56708556-56710651	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56650654..56653718-chr12:56708513..56712442,3	K562	blood:
2	chr12:56705654..56712950-chr12:56716015..56720160,8	MCF-7	breast:
3	chr12:56708314..56710826-chr12:56860625..56862676,3	K562	blood:
4	chr12:56707850..56716783-chr12:56721562..56730442,13	MCF-7	breast:
5	chr12:56708282..56711640-chr12:56860573..56864710,5	K562	blood:
6	chr12:56690986..56698275-chr12:56706607..56711958,20	MCF-7	breast:
7	chr12:56615078..56617831-chr12:56708226..56710350,2	MCF-7	breast:
8	chr12:56581557..56584767-chr12:56708519..56710789,3	K562	blood:
9	chr12:56708394..56711484-chr12:56860870..56863906,7	MCF-7	breast:
10	chr12:56708322..56710476-chr12:56739269..56741494,2	MCF-7	breast:
11	chr12:56707405..56709200-chr12:56752769..56755378,2	MCF-7	breast:
12	chr12:56707486..56713546-chr12:56723426..56730112,22	MCF-7	breast:
13	chr12:56708298..56710997-chr12:57029134..57031889,3	MCF-7	breast:
14	chr12:56510320..56513459-chr12:56707762..56709814,3	MCF-7	breast:
15	chr12:56707342..56711323-chr12:56861186..56863695,3	MCF-7	breast:
16	chr12:56659449..56661504-chr12:56708553..56711382,4	K562	blood:
17	chr12:56707797..56709815-chr12:56841516..56843203,2	MCF-7	breast:
18	chr12:56692256..56696973-chr12:56707335..56712231,9	K562	blood:
19	chr12:56650427..56652210-chr12:56707747..56710356,2	MCF-7	breast:
20	chr12:56683725..56686295-chr12:56708413..56711087,2	MCF-7	breast:
21	chr12:56700910..56706653-chr12:56706710..56711113,8	K562	blood:
22	chr12:56707245..56710317-chr12:56714317..56717689,3	MCF-7	breast:
23	chr12:56703600..56706626-chr12:56706710..56710673,5	K562	blood:
24	chr12:56690402..56700610-chr12:56705161..56712229,20	K562	blood:
25	chr12:56582213..56584132-chr12:56708371..56710862,2	MCF-7	breast:
26	chr12:56544606..56546956-chr12:56708353..56710252,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL23A-2	chr12:56708313-56708592	ENSG00000257303.1

No data

Variant related genes	Relation type
CNPY2	TF binding region
ENSG00000258199	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000257740	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000111602	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10876882	0.81[EUR][1000 genomes]
rs11171803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575234	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274490	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295772	0.91[ASN][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17118439	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2020854	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629447	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643623	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643626	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695782	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695789	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41392645	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542959	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773652	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773664	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773665	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808919	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs59295315	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs59295315	RP11-977G19.11	cis	Artery Tibial	GTEx
rs59295315	RP11-977G19.11	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56694800-56708800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56695000-56708600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:56695600-56708600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:56696400-56708600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:56697200-56708600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:56697800-56708600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:56697800-56708600	Strong transcription	Placenta	Placenta
8	chr12:56698000-56708600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:56698000-56708600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:56704800-56708600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:56704800-56708600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:56705000-56708600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:56705200-56708600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56705200-56708600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:56705200-56708600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:56705200-56708600	Weak transcription	Primary B cells from cord blood	blood
17	chr12:56705200-56708600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:56705200-56708600	Weak transcription	Colonic Mucosa	Colon
19	chr12:56705200-56708600	Weak transcription	Esophagus	oesophagus
20	chr12:56705200-56708600	Weak transcription	Fetal Kidney	kidney
21	chr12:56705200-56708600	Weak transcription	Gastric	stomach
22	chr12:56705200-56708600	Weak transcription	Left Ventricle	heart
23	chr12:56705200-56708600	Weak transcription	Lung	lung
24	chr12:56705200-56708600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:56705200-56708600	Weak transcription	Right Ventricle	heart
26	chr12:56705200-56708600	Weak transcription	Small Intestine	intestine
27	chr12:56705200-56708600	Weak transcription	Thymus	Thymus
28	chr12:56705200-56708600	Weak transcription	Spleen	Spleen
29	chr12:56705200-56708600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr12:56705200-56709000	Weak transcription	Aorta	Aorta
31	chr12:56705400-56708600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:56706400-56708800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:56707000-56708600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:56708000-56708600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:56708000-56708600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:56708000-56708600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:56708000-56708600	Genic enhancers	Liver	Liver
38	chr12:56708000-56708600	Strong transcription	Brain Anterior Caudate	brain
39	chr12:56708000-56708600	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr12:56708000-56708600	Strong transcription	Colon Smooth Muscle	Colon
41	chr12:56708000-56708600	Enhancers	Pancreas	Pancrea
42	chr12:56708000-56708800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:56708000-56708800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:56708000-56708800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:56708000-56708800	Enhancers	Fetal Heart	heart
46	chr12:56708200-56708600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
47	chr12:56708200-56708600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:56708200-56708600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:56708200-56708600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:56708200-56708600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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