Variant report

Variant	rs12121608
Chromosome Location	chr1:151515188-151515189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr1:151515148-151515566	Hela-S3	cervix:	n/a	n/a
2	BRCA1	chr1:151515144-151515500	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr1:151515128-151515523	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr1:151515041-151515632	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr1:151515184-151515550	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr1:151515067-151515425	IMR90	lung:	n/a	n/a
7	EP300	chr1:151515115-151515507	SK-N-SH_RA	brain:	n/a	n/a
8	MAX	chr1:151515082-151515678	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr1:151515160-151515310	SAEC	small airway:	n/a	n/a
10	CHD1	chr1:151511796-151515943	IMR90	lung:	n/a	n/a
11	REST	chr1:151515180-151515391	SK-N-SH	brain:	n/a	n/a
12	SIN3AK20	chr1:151515143-151515569	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr1:151514972-151515651	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr1:151514924-151515791	SK-N-SH	brain:	n/a	n/a
15	RCOR1	chr1:151515136-151515525	Hela-S3	cervix:	n/a	n/a
16	TAF1	chr1:151515051-151515380	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr1:151514939-151515594	MCF-7	breast:	n/a	chr1:151515168-151515179
18	POLR2A	chr1:151515052-151515606	SK-N-SH	brain:	n/a	n/a
19	MAX	chr1:151515058-151515631	SK-N-SH	brain:	n/a	n/a
20	TEAD4	chr1:151514868-151515646	SK-N-SH	brain:	n/a	n/a
21	FOSL2	chr1:151515137-151515632	SK-N-SH	brain:	n/a	n/a
22	SP1	chr1:151515090-151515672	A549	lung:	n/a	n/a
23	GATA3	chr1:151514759-151515855	SK-N-SH	brain:	n/a	chr1:151515168-151515179
24	GATA3	chr1:151514806-151515757	MCF-7	breast:	n/a	chr1:151515168-151515179
25	STAT3	chr1:151515181-151515382	MCF10A-Er-Src	breast:	n/a	chr1:151515270-151515282
26	EP300	chr1:151515124-151515559	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr1:151515046-151515751	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr1:151515135-151515562	SK-N-SH_RA	brain:	n/a	n/a
29	PBX3	chr1:151514938-151515799	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr1:151515011-151515735	A549	lung:	n/a	n/a
31	EP300	chr1:151514825-151515723	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr1:151515060-151515210	AG10803	skin:	n/a	n/a
33	MAX	chr1:151515133-151515584	Hela-S3	cervix:	n/a	n/a
34	GATA3	chr1:151514998-151515692	T-47D	breast:	n/a	chr1:151515168-151515179
35	NFIC	chr1:151514938-151515735	SK-N-SH	brain:	n/a	n/a
36	CEBPB	chr1:151515069-151515570	Hela-S3	cervix:	n/a	n/a
37	PBX3	chr1:151514988-151515757	SK-N-SH	brain:	n/a	n/a
38	JUND	chr1:151514937-151515663	SK-N-SH	brain:	n/a	n/a
39	NFIC	chr1:151514973-151515647	ECC-1	luminal epithelium:	n/a	n/a
40	FOSL2	chr1:151514960-151515727	SK-N-SH	brain:	n/a	n/a
41	SMC3	chr1:151515100-151515555	Hela-S3	cervix:	n/a	n/a
42	RXRA	chr1:151514987-151515659	SK-N-SH	brain:	n/a	chr1:151515318-151515327
43	SIN3AK20	chr1:151515089-151515536	SK-N-SH	brain:	n/a	n/a
44	TCF12	chr1:151515103-151515758	ECC-1	luminal epithelium:	n/a	n/a
45	GATA3	chr1:151515019-151515494	T-47D	breast:	n/a	chr1:151515168-151515179
46	TCF12	chr1:151514801-151515771	SK-N-SH	brain:	n/a	n/a
47	NFIC	chr1:151514966-151515702	SK-N-SH	brain:	n/a	n/a
48	JUND	chr1:151514926-151515685	SK-N-SH	brain:	n/a	n/a
49	RFX5	chr1:151515141-151515482	Hela-S3	cervix:	n/a	n/a
50	GATA3	chr1:151514861-151515829	A549	lung:	n/a	chr1:151515168-151515179

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
2	chr1:151421812..151434588-chr1:151506621..151515599,30	MCF-7	breast:
3	chr1:151510723..151515515-chr1:151802413..151805096,5	MCF-7	breast:
4	chr1:151514211..151516187-chr1:151541825..151543936,2	MCF-7	breast:
5	chr1:151514171..151515908-chr1:151540816..151544051,3	MCF-7	breast:
6	chr1:151510726..151515686-chr1:151583230..151586215,6	MCF-7	breast:
7	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
8	chr1:151510534..151515854-chr1:151533093..151539013,11	MCF-7	breast:
9	chr1:151513420..151515401-chr1:151965991..151967960,2	MCF-7	breast:
10	chr1:151513355..151515892-chr1:151812476..151814438,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR554	TF binding region
ENSG00000143442	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000229021	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1045298	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.81[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12121608	S100A6	cis	cerebellum	SCAN
rs12121608	OTUD7B	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151512400-151515600	Active TSS	Esophagus	oesophagus
2	chr1:151513400-151515800	Flanking Active TSS	Hela-S3	cervix
3	chr1:151513600-151515600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:151513800-151515200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:151513800-151515400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:151513800-151515600	Flanking Active TSS	Osteobl	bone
7	chr1:151513800-151519400	Weak transcription	Left Ventricle	heart
8	chr1:151514000-151515200	Weak transcription	Gastric	stomach
9	chr1:151514000-151515600	Enhancers	Aorta	Aorta
10	chr1:151514000-151515600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:151514000-151515800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:151514000-151515800	Flanking Active TSS	HSMM	muscle
13	chr1:151514000-151516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:151514000-151519400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:151514000-151519400	Weak transcription	HUVEC	blood vessel
16	chr1:151514200-151515200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:151514200-151515200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:151514200-151515400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:151514200-151515400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:151514200-151515600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:151514200-151515600	Enhancers	Brain Germinal Matrix	brain
22	chr1:151514200-151515600	Transcr. at gene 5' and 3'	NHEK	skin
23	chr1:151514200-151515800	Enhancers	Colon Smooth Muscle	Colon
24	chr1:151514200-151516200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:151514200-151516200	Flanking Active TSS	HSMMtube	muscle
26	chr1:151514200-151517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:151514200-151519400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:151514200-151519400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:151514200-151519400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:151514200-151519600	Weak transcription	Fetal Heart	heart
31	chr1:151514200-151519600	Weak transcription	Ovary	ovary
32	chr1:151514400-151515200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:151514400-151515200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:151514400-151515400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:151514400-151515400	Active TSS	Colonic Mucosa	Colon
36	chr1:151514400-151515400	Enhancers	Stomach Mucosa	stomach
37	chr1:151514400-151515600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:151514400-151515600	Enhancers	HepG2	liver
39	chr1:151514400-151516200	Enhancers	Adipose Nuclei	Adipose
40	chr1:151514400-151519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:151514400-151519600	Weak transcription	Psoas Muscle	Psoas
42	chr1:151514400-151519800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:151514400-151540800	Weak transcription	Brain Angular Gyrus	brain
44	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
45	chr1:151514600-151515200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:151514600-151515400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:151514600-151515400	Weak transcription	Fetal Brain Female	brain
48	chr1:151514600-151515400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:151514600-151515600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:151514600-151515600	Enhancers	Duodenum Mucosa	Duodenum

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