Variant report

Variant	rs11778396
Chromosome Location	chr8:125487766-125487767
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	SIN3AK20	chr8:125487295-125488062	A549	lung:	n/a	n/a
2	HCFC1	chr8:125485176-125489186	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr8:125487640-125487790	HCT-116	colon:	n/a	n/a
4	SRF	chr8:125486308-125487928	MCF-7	breast:	n/a	chr8:125487199-125487209
5	POLR2A	chr8:125486247-125487957	HL-60	blood:	n/a	n/a
6	TBP	chr8:125487376-125487876	HepG2	liver:	n/a	n/a
7	POLR2A	chr8:125485747-125488054	IMR90	lung:	n/a	n/a
8	EBF1	chr8:125486704-125487787	GM12878	blood:	n/a	chr8:125487584-125487593 chr8:125487582-125487595
9	TAF1	chr8:125487283-125487839	GM12891	blood:	n/a	n/a
10	POLR2A	chr8:125485952-125488016	K562	blood:	n/a	n/a
11	CTCF	chr8:125487700-125487850	A549	lung:	n/a	n/a
12	CTCF	chr8:125487700-125487850	HCM	heart:	n/a	n/a
13	ATF2	chr8:125487307-125487856	H1-hESC	embryonic stem cell:	n/a	n/a
14	CREB1	chr8:125486338-125487919	A549	lung:	n/a	chr8:125486892-125486905
15	CTCF	chr8:125487620-125487770	GM06990	blood:	n/a	n/a
16	CCNT2	chr8:125486416-125487980	K562	blood:	n/a	n/a
17	CTCF	chr8:125487660-125487810	GM12865	blood:	n/a	n/a
18	MYC	chr8:125485786-125488002	K562	blood:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
19	MYC	chr8:125485873-125487779	K562	blood:	n/a	chr8:125487056-125487066 chr8:125486876-125486885
20	SIN3AK20	chr8:125486383-125487771	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr8:125485774-125488828	Hela-S3	cervix:	n/a	n/a
22	TBP	chr8:125487445-125488777	GM12878	blood:	n/a	n/a
23	YY1	chr8:125486848-125487800	GM12892	blood:	n/a	chr8:125487050-125487064 chr8:125487056-125487070 chr8:125487030-125487052 chr8:125487204-125487213
24	RELA	chr8:125486045-125488107	GM10847	blood:	n/a	n/a
25	POLR2A	chr8:125486625-125487925	H1-hESC	embryonic stem cell:	n/a	n/a
26	MTA3	chr8:125487317-125488139	GM12878	blood:	n/a	n/a
27	CTCF	chr8:125487680-125487830	RPTEC	kidney:	n/a	n/a
28	POLR2A	chr8:125485124-125488693	MCF10A-Er-Src	breast:	n/a	n/a
29	MAX	chr8:125486236-125487971	A549	lung:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
30	SIN3A	chr8:125486091-125488880	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr8:125487700-125487850	HepG2	liver:	n/a	n/a
32	REST	chr8:125486009-125488915	H1-neurons	neurons:	n/a	chr8:125487587-125487597
33	TAF1	chr8:125486202-125487983	H1-neurons	neurons:	n/a	n/a
34	CTCF	chr8:125487649-125487829	Fibrobl	skin:	n/a	n/a
35	SMARCB1	chr8:125486277-125488006	Hela-S3	cervix:	n/a	n/a
36	CHD1	chr8:125486196-125489079	GM12878	blood:	n/a	n/a
37	POLR2A	chr8:125486192-125487903	GM12892	blood:	n/a	n/a
38	MYC	chr8:125487704-125487775	HepG2	liver:	n/a	n/a
39	GABPA	chr8:125486239-125488095	MCF-7	breast:	n/a	chr8:125487201-125487210 chr8:125487056-125487065 chr8:125486821-125486830 chr8:125486819-125486830 chr8:125486819-125486828
40	CHD2	chr8:125487431-125487863	H1-hESC	embryonic stem cell:	n/a	n/a
41	SP1	chr8:125487300-125488052	A549	lung:	n/a	chr8:125487679-125487693
42	POLR2A	chr8:125486019-125487991	GM19193	blood:	n/a	n/a
43	POLR2A	chr8:125486071-125488148	GM12878	blood:	n/a	n/a
44	YY1	chr8:125486271-125487822	ECC-1	luminal epithelium:	n/a	chr8:125487050-125487064 chr8:125487056-125487070 chr8:125487030-125487052 chr8:125487204-125487213
45	E2F6	chr8:125486265-125487965	K562	blood:	n/a	chr8:125487056-125487065 chr8:125486820-125486829 chr8:125487204-125487213
46	MAZ	chr8:125486316-125488031	Hela-S3	cervix:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
47	RCOR1	chr8:125486291-125487901	K562	blood:	n/a	n/a
48	KAP1	chr8:125487387-125489041	HEK293	kidney:	n/a	n/a
49	MYC	chr8:125486765-125487797	H1-hESC	embryonic stem cell:	n/a	chr8:125487056-125487066 chr8:125486876-125486885
50	JUN	chr8:125486154-125489145	K562	blood:	n/a	chr8:125486890-125486903 chr8:125487589-125487598

No.	Distal block	Cell Line	Cell type
1	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
2	chr8:98787245..98788965-chr8:125486458..125488343,2	MCF-7	breast:
3	chr8:125487371..125489055-chr8:125515121..125516817,2	MCF-7	breast:
4	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
5	chr8:125484053..125491713-chr8:125548138..125554442,21	K562	blood:
6	chr8:125487680..125490631-chr8:125553393..125557041,3	MCF-7	breast:
7	chr8:124818284..124820707-chr8:125487320..125489749,2	K562	blood:
8	chr2:28973922..28974429-chr8:125487612..125488451,2	Hela-S3	cervix:
9	chr6:10404647..10405264-chr8:125487109..125488035,2	Hela-S3	cervix:
10	chr8:125485971..125490407-chr8:125553790..125556730,4	MCF-7	breast:
11	chr8:124407395..124409039-chr8:125486191..125487874,2	MCF-7	breast:
12	chr20:46128886..46131139-chr8:125486478..125488515,2	MCF-7	breast:
13	chr8:125485694..125488622-chr8:125558773..125560275,2	MCF-7	breast:
14	chr8:125484651..125489587-chr8:125535041..125543731,11	K562	blood:
15	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
16	chr13:27997218..27999271-chr8:125486263..125488862,2	MCF-7	breast:
17	chr8:125483604..125491110-chr8:125548591..125554086,23	K562	blood:
18	chr8:125485539..125488439-chr8:125531952..125535064,5	MCF-7	breast:
19	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
20	chr8:125487117..125490518-chr8:125542261..125547751,5	K562	blood:
21	chr8:125484977..125488762-chr8:125516872..125524765,8	MCF-7	breast:
22	chr1:202775016..202777595-chr8:125486328..125488390,2	MCF-7	breast:
23	chr8:124835781..124838013-chr8:125487018..125488590,2	MCF-7	breast:
24	chr8:125487104..125489610-chr8:126009410..126011098,2	MCF-7	breast:
25	chr1:155197003..155197581-chr8:125487003..125487937,2	Hela-S3	cervix:
26	chr3:49202004..49204374-chr8:125485548..125487898,2	MCF-7	breast:
27	chr8:125487492..125489974-chr8:125525285..125527024,3	K562	blood:
28	chr8:125484298..125489708-chr8:125549185..125553061,9	MCF-7	breast:
29	chr8:124780302..124782573-chr8:125486403..125488504,7	MCF-7	breast:
30	chr8:125485755..125491202-chr8:125535208..125540184,8	MCF-7	breast:
31	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:

Variant related genes	Relation type
RNF139-AS1	TF binding region
ENSG00000170873	Chromatin interaction
ENSG00000156802	Chromatin interaction
ENSG00000117139	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000104341	Chromatin interaction
ENSG00000104549	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000176853	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000122034	Chromatin interaction
ENSG00000137203	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000253513	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10094916	1.00[YRI][hapmap]
rs10103773	1.00[YRI][hapmap]
rs10110655	0.86[YRI][hapmap]
rs13255599	1.00[YRI][hapmap]
rs16899688	0.91[YRI][hapmap]
rs3829035	0.86[YRI][hapmap]
rs6470253	1.00[YRI][hapmap]
rs6470254	1.00[YRI][hapmap]
rs7010757	1.00[YRI][hapmap]
rs7015374	1.00[YRI][hapmap]
rs7835397	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS 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	84 gene(s)	inside rSNPs	diseases
2	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
4	esv3339866	chr8:125485996-125488544	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11778396	TRMT12	cis	Whole Blood	GTEx
rs11778396	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125484000-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:125484200-125488600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:125484200-125488600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:125484200-125488800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:125484200-125488800	Active TSS	HSMM	muscle
6	chr8:125484200-125489200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:125484200-125489400	Active TSS	K562	blood
8	chr8:125484400-125488400	Active TSS	Muscle Satellite Cultured Cells	--
9	chr8:125484400-125488800	Active TSS	NHLF	lung
10	chr8:125484400-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:125484400-125489600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:125484600-125488600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr8:125484600-125488600	Active TSS	NHDF-Ad	bronchial
14	chr8:125484600-125489200	Active TSS	Right Ventricle	heart
15	chr8:125484800-125488400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr8:125484800-125488400	Active TSS	HSMMtube	muscle
17	chr8:125484800-125488400	Active TSS	NH-A	brain
18	chr8:125484800-125489000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr8:125484800-125489200	Active TSS	Aorta	Aorta
20	chr8:125484800-125489200	Active TSS	Ovary	ovary
21	chr8:125484800-125489200	Active TSS	A549	lung
22	chr8:125484800-125489400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr8:125484800-125489400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr8:125484800-125489400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr8:125484800-125490200	Active TSS	GM12878-XiMat	blood
26	chr8:125485000-125487800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:125485000-125487800	Active TSS	Hela-S3	cervix
28	chr8:125485000-125488200	Active TSS	Fetal Kidney	kidney
29	chr8:125485000-125488800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:125485000-125488800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:125485000-125488800	Active TSS	Fetal Intestine Large	intestine
32	chr8:125485000-125488800	Active TSS	Fetal Intestine Small	intestine
33	chr8:125485000-125488800	Active TSS	HMEC	breast
34	chr8:125485000-125488800	Active TSS	NHEK	skin
35	chr8:125485200-125488400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:125485200-125488600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:125485200-125488600	Active TSS	Placenta	Placenta
38	chr8:125485200-125489000	Active TSS	Fetal Muscle Trunk	muscle
39	chr8:125485200-125489200	Active TSS	H1 Cell Line	embryonic stem cell
40	chr8:125485400-125488000	Active TSS	Fetal Muscle Leg	muscle
41	chr8:125485400-125488200	Active TSS	Gastric	stomach
42	chr8:125485400-125488200	Active TSS	Lung	lung
43	chr8:125485400-125488800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr8:125485400-125488800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr8:125485400-125488800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr8:125485400-125488800	Active TSS	Colonic Mucosa	Colon
47	chr8:125485400-125488800	Active TSS	Left Ventricle	heart
48	chr8:125485600-125488000	Active TSS	Rectal Smooth Muscle	rectum
49	chr8:125485600-125488000	Active TSS	Osteobl	bone
50	chr8:125485600-125488200	ZNF genes & repeats	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links