Variant report

Variant	rs11204844
Chromosome Location	chr1:151515458-151515459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 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	MYC	chr1:151515235-151515589	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:151515200-151515569	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr1:151515128-151515523	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr1:151515208-151515564	Hela-S3	cervix:	n/a	n/a
7	NFIC	chr1:151515041-151515632	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr1:151515184-151515550	Hela-S3	cervix:	n/a	n/a
9	EP300	chr1:151515115-151515507	SK-N-SH_RA	brain:	n/a	n/a
10	MAX	chr1:151515082-151515678	SK-N-SH	brain:	n/a	n/a
11	CHD1	chr1:151511796-151515943	IMR90	lung:	n/a	n/a
12	SIN3AK20	chr1:151515143-151515569	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr1:151515198-151515630	MCF10A-Er-Src	breast:	n/a	n/a
14	TEAD4	chr1:151514972-151515651	ECC-1	luminal epithelium:	n/a	n/a
15	ELK1	chr1:151515224-151515566	Hela-S3	cervix:	n/a	n/a
16	EP300	chr1:151514924-151515791	SK-N-SH	brain:	n/a	n/a
17	RCOR1	chr1:151515136-151515525	Hela-S3	cervix:	n/a	n/a
18	ZKSCAN1	chr1:151515192-151515720	Hela-S3	cervix:	n/a	n/a
19	GATA3	chr1:151514939-151515594	MCF-7	breast:	n/a	chr1:151515168-151515179
20	POLR2A	chr1:151515052-151515606	SK-N-SH	brain:	n/a	n/a
21	MAX	chr1:151515058-151515631	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr1:151514868-151515646	SK-N-SH	brain:	n/a	n/a
23	FOSL2	chr1:151515137-151515632	SK-N-SH	brain:	n/a	n/a
24	SP1	chr1:151515090-151515672	A549	lung:	n/a	n/a
25	GATA3	chr1:151514759-151515855	SK-N-SH	brain:	n/a	chr1:151515168-151515179
26	GATA3	chr1:151514806-151515757	MCF-7	breast:	n/a	chr1:151515168-151515179
27	EP300	chr1:151515124-151515559	Hela-S3	cervix:	n/a	n/a
28	MYC	chr1:151515268-151515584	MCF10A-Er-Src	breast:	n/a	n/a
29	TCF12	chr1:151515046-151515751	ECC-1	luminal epithelium:	n/a	n/a
30	TBP	chr1:151515190-151515546	Hela-S3	cervix:	n/a	n/a
31	EP300	chr1:151515135-151515562	SK-N-SH_RA	brain:	n/a	n/a
32	PBX3	chr1:151514938-151515799	SK-N-SH	brain:	n/a	n/a
33	TCF12	chr1:151515011-151515735	A549	lung:	n/a	n/a
34	EP300	chr1:151514825-151515723	SK-N-SH	brain:	n/a	n/a
35	MAX	chr1:151515133-151515584	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr1:151514998-151515692	T-47D	breast:	n/a	chr1:151515168-151515179
37	ZNF143	chr1:151515225-151515568	Hela-S3	cervix:	n/a	n/a
38	NFIC	chr1:151514938-151515735	SK-N-SH	brain:	n/a	n/a
39	MAFK	chr1:151515193-151515460	Hela-S3	cervix:	n/a	n/a
40	CEBPB	chr1:151515069-151515570	Hela-S3	cervix:	n/a	n/a
41	PBX3	chr1:151514988-151515757	SK-N-SH	brain:	n/a	n/a
42	JUND	chr1:151514937-151515663	SK-N-SH	brain:	n/a	n/a
43	FOS	chr1:151515273-151515466	MCF10A-Er-Src	breast:	n/a	n/a
44	CHD2	chr1:151515209-151515517	Hela-S3	cervix:	n/a	n/a
45	NFIC	chr1:151514973-151515647	ECC-1	luminal epithelium:	n/a	n/a
46	FOSL2	chr1:151514960-151515727	SK-N-SH	brain:	n/a	n/a
47	SMC3	chr1:151515100-151515555	Hela-S3	cervix:	n/a	n/a
48	RXRA	chr1:151514987-151515659	SK-N-SH	brain:	n/a	chr1:151515318-151515327
49	SIN3AK20	chr1:151515089-151515536	SK-N-SH	brain:	n/a	n/a
50	USF2	chr1:151515225-151515633	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 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	chr1:151515446..151517713-chr1:151630494..151632395,2	MCF-7	breast:
4	chr1:151510723..151515515-chr1:151802413..151805096,5	MCF-7	breast:
5	chr1:151514211..151516187-chr1:151541825..151543936,2	MCF-7	breast:
6	chr1:151514171..151515908-chr1:151540816..151544051,3	MCF-7	breast:
7	chr1:151510726..151515686-chr1:151583230..151586215,6	MCF-7	breast:
8	chr1:151510534..151515854-chr1:151533093..151539013,11	MCF-7	breast:
9	chr1:151513355..151515892-chr1:151812476..151814438,2	MCF-7	breast:

No data

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

Extended variants
information (count: 12 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12044926	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1418823	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs16833376	0.83[EUR][1000 genomes]
rs17640579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17640598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35342887	0.83[EUR][1000 genomes]
rs55840963	0.84[EUR][1000 genomes]
rs6686193	0.81[EUR][1000 genomes]
rs72692715	0.85[EUR][1000 genomes]
rs72692719	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11204844	S100A9	cis	parietal	SCAN
rs11204844	LCE3B	cis	cerebellum	SCAN
rs11204844	C1orf230	cis	parietal	SCAN
rs11204844	GATAD2B	cis	parietal	SCAN
rs11204844	IVL	cis	parietal	SCAN
rs11204844	KPRP	cis	parietal	SCAN
rs11204844	CGN	cis	cerebellum	SCAN
rs11204844	LCE1C	cis	cerebellum	SCAN
rs11204844	MLLT11	cis	parietal	SCAN

Chromatin state (count:79 , 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	chr1:151513800-151515600	Flanking Active TSS	Osteobl	bone
5	chr1:151513800-151519400	Weak transcription	Left Ventricle	heart
6	chr1:151514000-151515600	Enhancers	Aorta	Aorta
7	chr1:151514000-151515600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:151514000-151515800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:151514000-151515800	Flanking Active TSS	HSMM	muscle
10	chr1:151514000-151516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:151514000-151519400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151514000-151519400	Weak transcription	HUVEC	blood vessel
13	chr1:151514200-151515600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:151514200-151515600	Enhancers	Brain Germinal Matrix	brain
15	chr1:151514200-151515600	Transcr. at gene 5' and 3'	NHEK	skin
16	chr1:151514200-151515800	Enhancers	Colon Smooth Muscle	Colon
17	chr1:151514200-151516200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:151514200-151516200	Flanking Active TSS	HSMMtube	muscle
19	chr1:151514200-151517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:151514200-151519400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:151514200-151519400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:151514200-151519400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:151514200-151519600	Weak transcription	Fetal Heart	heart
24	chr1:151514200-151519600	Weak transcription	Ovary	ovary
25	chr1:151514400-151515600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:151514400-151515600	Enhancers	HepG2	liver
27	chr1:151514400-151516200	Enhancers	Adipose Nuclei	Adipose
28	chr1:151514400-151519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:151514400-151519600	Weak transcription	Psoas Muscle	Psoas
30	chr1:151514400-151519800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:151514400-151540800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
33	chr1:151514600-151515600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:151514600-151515600	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:151514600-151515600	Flanking Active TSS	Placenta	Placenta
36	chr1:151514600-151515600	Enhancers	Stomach Smooth Muscle	stomach
37	chr1:151514600-151515800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:151514600-151515800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:151514600-151515800	Enhancers	HMEC	breast
40	chr1:151514600-151516000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:151514600-151516200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:151514600-151516200	Enhancers	NHDF-Ad	bronchial
43	chr1:151514600-151516400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:151514600-151516400	Enhancers	Pancreas	Pancrea
45	chr1:151514600-151516600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:151514600-151519200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:151514600-151519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:151514600-151519400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:151514600-151519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:151514600-151519600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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