Variant report

Variant	rs57870697
Chromosome Location	chr12:56752874-56752875
allele	A/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	chr12:56752530-56753102	GM12891	blood:	n/a	n/a
2	TAF1	chr12:56752625-56752894	GM12878	blood:	n/a	n/a
3	STAT2	chr12:56752586-56752931	K562	blood:	n/a	chr12:56752780-56752791 chr12:56752778-56752793
4	MYC	chr12:56752768-56752913	MCF10A-Er-Src	breast:	n/a	chr12:56752853-56752862 chr12:56752851-56752864
5	MXI1	chr12:56752439-56754755	IMR90	lung:	n/a	n/a
6	USF1	chr12:56752703-56753028	SK-N-SH_RA	brain:	n/a	n/a
7	RUNX3	chr12:56752576-56753042	GM12878	blood:	n/a	chr12:56752837-56752846
8	POU2F2	chr12:56752616-56753006	GM12878	blood:	n/a	n/a
9	MXI1	chr12:56752651-56752976	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:56752615-56753090	U87	brain:	n/a	n/a
11	POLR2A	chr12:56752472-56753057	U87	brain:	n/a	n/a
12	CEBPB	chr12:56752686-56753001	Hela-S3	cervix:	n/a	n/a
13	USF2	chr12:56752774-56752981	GM12878	blood:	n/a	chr12:56752851-56752862
14	POLR2A	chr12:56752444-56752952	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:56752615-56753049	U87	brain:	n/a	n/a
16	POU2F2	chr12:56752503-56753012	GM12878	blood:	n/a	n/a
17	RUNX3	chr12:56752589-56752997	GM12878	blood:	n/a	chr12:56752837-56752846
18	CEBPB	chr12:56752678-56753247	IMR90	lung:	n/a	n/a
19	POLR2A	chr12:56752771-56752905	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:56752506-56753007	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:56752553-56752997	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:56752460-56753020	GM12878	blood:	n/a	n/a
23	MAZ	chr12:56752517-56754615	IMR90	lung:	n/a	chr12:56752853-56752862 chr12:56752851-56752864 chr12:56753860-56753870
24	USF1	chr12:56752686-56753002	SK-N-SH_RA	brain:	n/a	n/a
25	POLR2A	chr12:56752598-56753112	SK-N-SH	brain:	n/a	n/a
26	MXI1	chr12:56752383-56754900	SK-N-SH	brain:	n/a	n/a
27	MEF2A	chr12:56752534-56752950	GM12878	blood:	n/a	n/a
28	IRF1	chr12:56752643-56753212	K562	blood:	n/a	chr12:56752779-56752791 chr12:56752776-56752790 chr12:56752785-56752792 chr12:56752777-56752791 chr12:56752780-56752791 chr12:56752777-56752794 chr12:56752778-56752791 chr12:56752778-56752791 chr12:56752779-56752796 chr12:56752778-56752791 chr12:56752778-56752792 chr12:56752779-56752793 chr12:56752778-56752791 chr12:56752772-56752792 chr12:56752780-56752790
29	POLR2A	chr12:56752600-56753036	GM12878	blood:	n/a	n/a
30	MAX	chr12:56752590-56753029	SK-N-SH	brain:	n/a	chr12:56752853-56752862 chr12:56752851-56752864
31	USF1	chr12:56752654-56753264	SK-N-SH	brain:	n/a	n/a
32	TCF3	chr12:56752550-56752910	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:56752589-56753121	ProgFib	skin:	n/a	n/a
34	POLR2A	chr12:56752777-56752995	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr12:56752792-56753045	SK-N-SH	brain:	n/a	n/a
36	MYC	chr12:56752793-56752976	MCF10A-Er-Src	breast:	n/a	chr12:56752853-56752862 chr12:56752851-56752864
37	NFIC	chr12:56752633-56753056	GM12878	blood:	n/a	n/a
38	USF2	chr12:56752711-56753018	Hela-S3	cervix:	n/a	chr12:56752851-56752862

No.	Distal block	Cell Line	Cell type
1	chr12:56692844..56694966-chr12:56751203..56753626,2	K562	blood:
2	chr12:56707405..56709200-chr12:56752769..56755378,2	MCF-7	breast:
3	chr12:56752493..56755436-chr12:56859728..56862331,2	MCF-7	breast:
4	chr12:56752523..56755343-chr12:56862151..56864248,2	MCF-7	breast:
5	chr12:56752238..56754707-chr12:56756251..56758252,3	MCF-7	breast:
6	chr12:56743017..56746738-chr12:56752337..56755444,3	K562	blood:
7	chr12:56727184..56732099-chr12:56751309..56755132,9	K562	blood:
8	chr12:56751886..56753976-chr12:56841675..56844416,2	MCF-7	breast:
9	chr12:56725978..56729877-chr12:56750632..56755261,5	MCF-7	breast:
10	chr12:56747914..56751304-chr12:56752091..56755313,3	MCF-7	breast:
11	chr12:56692915..56694824-chr12:56751015..56754096,3	MCF-7	breast:
12	chr12:56726126..56729287-chr12:56751281..56753885,4	MCF-7	breast:
13	chr12:56752241..56754348-chr12:56862536..56866569,3	K562	blood:
14	chr12:56748502..56750410-chr12:56752086..56754336,2	MCF-7	breast:

Variant related genes	Relation type
STAT2	TF binding region
ENSG00000170581	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000252206	Chromatin interaction
ENSG00000175336	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000135473	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11171803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575234	0.94[EUR][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1274493	0.88[EUR][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17118431	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17118439	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2020854	0.94[EUR][1000 genomes]
rs2066807	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2066808	0.88[EUR][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2371494	0.88[EUR][1000 genomes]
rs2629447	0.88[EUR][1000 genomes]
rs2643626	0.88[EUR][1000 genomes]
rs2695782	0.88[EUR][1000 genomes]
rs2695788	0.88[EUR][1000 genomes]
rs2695789	0.88[EUR][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41392645	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60542959	0.84[EUR][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs703830	0.88[EUR][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773652	0.81[EUR][1000 genomes]
rs773664	0.88[EUR][1000 genomes]
rs773665	0.88[EUR][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][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
rs57870697	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs57870697	RP11-977G19.11	cis	Artery Tibial	GTEx
rs57870697	RP11-977G19.11	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56733000-56753200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56749400-56753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:56750000-56753000	Weak transcription	Small Intestine	intestine
4	chr12:56750400-56753000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:56750400-56753000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:56750400-56753200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:56750400-56753400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:56750400-56753400	Weak transcription	Esophagus	oesophagus
9	chr12:56751400-56753000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:56751600-56753000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:56751600-56753000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:56751600-56753000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr12:56751600-56755000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:56751600-56755000	Active TSS	GM12878-XiMat	blood
15	chr12:56752000-56754800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:56752200-56753000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:56752200-56753000	Enhancers	Left Ventricle	heart
18	chr12:56752200-56753000	Enhancers	Spleen	Spleen
19	chr12:56752200-56753200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:56752200-56753200	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr12:56752200-56753200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr12:56752200-56753200	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr12:56752200-56753400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:56752200-56753400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:56752200-56755000	Active TSS	HSMMtube	muscle
26	chr12:56752400-56753000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:56752400-56753000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:56752400-56753000	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr12:56752400-56753000	Enhancers	Placenta	Placenta
30	chr12:56752400-56753000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:56752400-56753000	Flanking Active TSS	K562	blood
32	chr12:56752400-56753200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr12:56752400-56753200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:56752400-56753200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr12:56752400-56753200	Flanking Active TSS	Fetal Lung	lung
36	chr12:56752400-56753200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr12:56752400-56753200	Flanking Active TSS	NH-A	brain
38	chr12:56752400-56753400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:56752400-56753400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr12:56752400-56753400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:56752400-56753400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr12:56752400-56753400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr12:56752400-56753400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr12:56752400-56753400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:56752400-56753400	Flanking Active TSS	Liver	Liver
46	chr12:56752400-56753400	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr12:56752400-56753400	Flanking Active TSS	Thymus	Thymus
48	chr12:56752400-56753400	Flanking Active TSS	Dnd41	blood
49	chr12:56752400-56753400	Flanking Active TSS	Hela-S3	cervix
50	chr12:56752400-56753400	Flanking Active TSS	NHEK	skin

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