Variant report

Variant	rs11803990
Chromosome Location	chr1:150539706-150539707
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	EBF1	chr1:150539670-150541315	GM12878	blood:	n/a	n/a
2	NFATC1	chr1:150539680-150541136	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:150539585-150540995	GM12878	blood:	n/a	n/a
4	MEF2A	chr1:150539650-150540454	GM12878	blood:	n/a	chr1:150540240-150540248
5	MAX	chr1:150539694-150540934	GM12878	blood:	n/a	n/a
6	RELA	chr1:150539687-150540531	GM15510	blood:	n/a	n/a
7	POLR2A	chr1:150538973-150541826	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:150538992-150539987	Hela-S3	cervix:	n/a	n/a
9	POU2F2	chr1:150539596-150540871	GM12891	blood:	n/a	chr1:150540604-150540615
10	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
12	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
13	NFIC	chr1:150539585-150541059	GM12878	blood:	n/a	n/a
14	POU2F2	chr1:150539690-150540595	GM12878	blood:	n/a	n/a
15	CHD2	chr1:150539706-150540975	GM12878	blood:	n/a	chr1:150540331-150540341
16	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
17	PAX5	chr1:150539668-150540509	GM12878	blood:	n/a	n/a
18	MEF2C	chr1:150539624-150540430	GM12878	blood:	n/a	chr1:150540240-150540248
19	ZNF384	chr1:150539680-150540431	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
21	SP1	chr1:150539703-150540765	GM12878	blood:	n/a	chr1:150540582-150540593 chr1:150540329-150540341 chr1:150540331-150540340
22	NFIC	chr1:150539583-150540902	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:150539675-150540003	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
25	EBF1	chr1:150539664-150540109	GM12878	blood:	n/a	n/a
26	BCLAF1	chr1:150539702-150540934	GM12878	blood:	n/a	chr1:150540625-150540634
27	POLR2A	chr1:150539052-150541758	K562	blood:	n/a	n/a
28	POLR2A	chr1:150539702-150540985	Raji	blood:	n/a	n/a
29	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:150539558-150541740	GM19193	blood:	n/a	n/a
31	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
32	CEBPB	chr1:150539311-150540800	GM12878	blood:	n/a	n/a
33	MTA3	chr1:150539566-150541051	GM12878	blood:	n/a	n/a
34	YY1	chr1:150539652-150540466	GM12878	blood:	n/a	chr1:150540329-150540340
35	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
36	PML	chr1:150539572-150541533	GM12878	blood:	n/a	n/a
37	STAT5A	chr1:150539671-150540924	GM12878	blood:	n/a	chr1:150540015-150540029 chr1:150540014-150540029 chr1:150540625-150540636
38	IRF4	chr1:150539607-150540945	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:150539144-150541805	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:150539636-150544211	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr1:150539700-150539850	GM12872	blood:	n/a	n/a
45	POLR2A	chr1:150539629-150541828	K562	blood:	n/a	n/a
46	POLR2A	chr1:150539644-150540534	GM12891	blood:	n/a	n/a
47	TAF1	chr1:150539632-150540244	GM12878	blood:	n/a	n/a
48	PAX5	chr1:150539585-150540634	GM12878	blood:	n/a	chr1:150540625-150540634
49	STAT5A	chr1:150539563-150540679	GM12878	blood:	n/a	chr1:150540015-150540029 chr1:150540014-150540029 chr1:150540625-150540636
50	RUNX3	chr1:150539594-150541035	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150538740..150540797-chr1:150784272..150785983,2	MCF-7	breast:
2	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
3	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
4	chr1:150539334..150542207-chr1:150782861..150785483,3	K562	blood:
5	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
6	chr1:150520253..150522845-chr1:150539005..150541527,2	MCF-7	breast:
7	chr1:150459936..150462426-chr1:150537781..150540425,2	K562	blood:
8	chr1:150539334..150542207-chr1:150782861..150785483,4	K562	blood:

Variant related genes	Relation type
RN7SL473P	TF binding region
ENSG00000225996	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000143382	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs35392872	0.83[EUR][1000 genomes]

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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases
3	nsv527379	chr1:150527354-150542128	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11803990	CTSS	cis	putamen	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150534600-150540200	Enhancers	Pancreas	Pancrea
3	chr1:150534600-150542600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:150534600-150542600	Enhancers	Lung	lung
5	chr1:150534800-150539800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:150534800-150540400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:150535000-150539800	Enhancers	Fetal Lung	lung
8	chr1:150535000-150540000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:150535000-150540200	Enhancers	Left Ventricle	heart
10	chr1:150535000-150542200	Enhancers	Placenta	Placenta
11	chr1:150535200-150539800	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:150535200-150540000	Enhancers	Fetal Intestine Large	intestine
13	chr1:150535200-150540000	Enhancers	Psoas Muscle	Psoas
14	chr1:150535200-150540000	Enhancers	Right Atrium	heart
15	chr1:150535200-150541000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:150535200-150541800	Enhancers	Small Intestine	intestine
17	chr1:150535400-150539800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:150535400-150540200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:150535400-150540400	Enhancers	Fetal Heart	heart
20	chr1:150535600-150540200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:150535800-150539800	Enhancers	HSMMtube	muscle
22	chr1:150536000-150540800	Enhancers	Stomach Mucosa	stomach
23	chr1:150536600-150539800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:150536600-150540600	Weak transcription	Fetal Brain Female	brain
25	chr1:150536800-150539800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:150536800-150539800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:150536800-150539800	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:150536800-150539800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:150536800-150539800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:150536800-150539800	Weak transcription	Brain Germinal Matrix	brain
31	chr1:150536800-150540400	Weak transcription	Fetal Brain Male	brain
32	chr1:150537200-150540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:150537400-150539800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:150537600-150539800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:150537600-150540000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:150537800-150539800	Weak transcription	Hela-S3	cervix
37	chr1:150538200-150540200	Enhancers	Spleen	Spleen
38	chr1:150538200-150540400	Enhancers	Right Ventricle	heart
39	chr1:150538400-150540200	Enhancers	Brain Anterior Caudate	brain
40	chr1:150538600-150539800	Weak transcription	NHEK	skin
41	chr1:150538600-150540000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:150538800-150539800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:150538800-150539800	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr1:150538800-150539800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:150538800-150540000	Enhancers	Aorta	Aorta
46	chr1:150538800-150540000	Enhancers	Fetal Stomach	stomach
47	chr1:150538800-150541800	Flanking Active TSS	GM12878-XiMat	blood
48	chr1:150538800-150541800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr1:150538800-150543800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr1:150538800-150543800	Enhancers	HMEC	breast

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