Variant report

Variant	rs17298912
Chromosome Location	chr8:125573374-125573375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:125573280-125573430	HAc	cerebellar:	n/a	n/a
2	CTCF	chr8:125573280-125573430	BE2_C	brain:	n/a	n/a
3	CTCF	chr8:125573300-125573450	MCF-7	breast:	n/a	n/a
4	CTCF	chr8:125573300-125573450	NHEK	skin:	n/a	n/a
5	CTCF	chr8:125573320-125573470	SAEC	small airway:	n/a	n/a
6	CTCF	chr8:125573260-125573410	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr8:125573300-125573450	HPAF	blood vessel:	n/a	n/a
8	CTCF	chr8:125573374-125573471	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr8:125573300-125573450	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr8:125573340-125573490	AoAF	blood vessel:	n/a	n/a
11	CTCF	chr8:125573340-125573490	NHEK	skin:	n/a	n/a
12	CTCF	chr8:125573240-125573390	HVMF	connective:	n/a	n/a
13	CTCF	chr8:125573300-125573450	HCT-116	colon:	n/a	n/a
14	CTCF	chr8:125573240-125573390	HMF	breast:	n/a	n/a
15	CTCF	chr8:125573300-125573450	GM12875	blood:	n/a	n/a
16	CTCF	chr8:125573240-125573390	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125572673..125575871-chr8:125577015..125582400,6	K562	blood:
3	chr8:125543458..125545211-chr8:125571140..125573606,2	MCF-7	breast:
4	chr8:125551424..125552952-chr8:125573257..125575450,2	K562	blood:
5	chr8:125501995..125503698-chr8:125571689..125573791,2	K562	blood:
6	chr8:125570451..125574343-chr8:125825804..125829124,4	K562	blood:
7	chr8:125554525..125556837-chr8:125571840..125574093,4	K562	blood:
8	chr8:125570314..125572061-chr8:125572775..125574818,2	MCF-7	breast:
9	chr8:125539308..125541314-chr8:125571807..125574800,2	MCF-7	breast:
10	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
11	chr8:125573332..125574424-chr8:125592832..125593703,3	MCF-7	breast:
12	chr8:125571310..125574209-chr8:125585133..125590105,4	MCF-7	breast:
13	chr8:125570946..125573544-chr8:125575024..125576793,2	MCF-7	breast:
14	chr8:125554525..125556396-chr8:125571840..125574093,2	K562	blood:
15	chr8:125572358..125574259-chr8:125739651..125742018,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000170873	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10505446	0.86[CEU][hapmap]
rs17298759	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298884	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299030	0.92[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299208	0.93[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299341	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300503	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17372350	1.00[CEU][hapmap]
rs17372901	1.00[ASN][1000 genomes]
rs4585740	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470248	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7003602	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830235	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv465801	chr8:125565328-125576681	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv612145	chr8:125565328-125576681	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv465802	chr8:125570144-125576681	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv612146	chr8:125570144-125576681	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17298912	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
3	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
5	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:125554400-125574200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
9	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
10	chr8:125554600-125574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr8:125555200-125574000	Strong transcription	Placenta	Placenta
14	chr8:125555200-125575000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr8:125555200-125575200	Strong transcription	Brain Cingulate Gyrus	brain
16	chr8:125555600-125574200	Strong transcription	Primary T cells from cord blood	blood
17	chr8:125556000-125574200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:125556200-125575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr8:125558000-125575600	Weak transcription	Stomach Mucosa	stomach
21	chr8:125558200-125573600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:125560400-125575000	Weak transcription	Right Atrium	heart
23	chr8:125561200-125575200	Strong transcription	HepG2	liver
24	chr8:125561400-125575000	Strong transcription	Adipose Nuclei	Adipose
25	chr8:125561400-125575600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:125561600-125573400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:125561600-125575000	Strong transcription	Liver	Liver
28	chr8:125563600-125574400	Strong transcription	Right Ventricle	heart
29	chr8:125563600-125575600	Strong transcription	Fetal Stomach	stomach
30	chr8:125564000-125574000	Weak transcription	K562	blood
31	chr8:125564000-125574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr8:125564000-125575600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr8:125564200-125574000	Strong transcription	Brain Germinal Matrix	brain
34	chr8:125564400-125576800	Strong transcription	Fetal Intestine Small	intestine
35	chr8:125564800-125573400	Weak transcription	Hela-S3	cervix
36	chr8:125566000-125575000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr8:125566000-125576400	Weak transcription	GM12878-XiMat	blood
38	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
39	chr8:125566200-125575800	Weak transcription	NHDF-Ad	bronchial
40	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:125566400-125573800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr8:125566400-125574000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr8:125566400-125574200	Weak transcription	Psoas Muscle	Psoas
44	chr8:125566400-125575000	Weak transcription	Dnd41	blood
45	chr8:125566400-125575800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr8:125566400-125575800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:125566400-125577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr8:125566400-125577800	Weak transcription	Small Intestine	intestine
49	chr8:125566400-125600600	Weak transcription	NHEK	skin
50	chr8:125566600-125573800	Weak transcription	H1 Cell Line	embryonic stem cell

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