Variant report

Variant	rs1047581
Chromosome Location	chr11:33724992-33724993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:33724950-33725761	A549	lung:	n/a	n/a
2	POLR2A	chr11:33724627-33725193	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr11:33722124-33725044	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:33724692-33725151	HUVEC	blood vessel:	n/a	n/a
5	FOS	chr11:33724848-33725048	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr11:33724733-33725009	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr11:33724847-33725016	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr11:33724918-33725781	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:33724817-33726519	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:33724703-33727275	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:33724991-33726399	K562	blood:	n/a	n/a
12	POLR2A	chr11:33724778-33725682	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr11:33724634-33727795	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:33724956-33725484	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr11:33724921-33725862	GM12891	blood:	n/a	n/a
16	POLR2A	chr11:33722026-33728243	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr11:33724741-33725074	HCT-116	colon:	n/a	n/a
18	POLR2A	chr11:33724925-33725863	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:33724933-33725766	A549	lung:	n/a	n/a
20	POLR2A	chr11:33724634-33727281	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr11:33724719-33725154	U87	brain:	n/a	n/a
22	POLR2A	chr11:33724885-33727788	GM12892	blood:	n/a	n/a
23	POLR2A	chr11:33724939-33727198	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:33724744-33729888	K562	blood:	n/a	n/a
25	POLR2A	chr11:33724898-33725189	K562	blood:	n/a	n/a
26	POLR2A	chr11:33724876-33726501	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr11:33721095-33724992	IMR90	lung:	n/a	n/a
28	POLR2A	chr11:33724792-33725526	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:33724939-33726929	GM12892	blood:	n/a	n/a
30	JUND	chr11:33724910-33725735	A549	lung:	n/a	n/a
31	CEBPB	chr11:33724660-33725003	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:33724640-33726521	U87	brain:	n/a	n/a
33	POLR2A	chr11:33720387-33727134	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr11:33724805-33726238	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr11:33724864-33726933	GM12892	blood:	n/a	n/a
36	FOSL2	chr11:33724969-33725688	HepG2	liver:	n/a	n/a
37	POLR2A	chr11:33724796-33726461	MCF-7	breast:	n/a	n/a
38	POLR2A	chr11:33724737-33729905	A549	lung:	n/a	n/a
39	POLR2A	chr11:33724643-33727840	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr11:33720521-33727789	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:33714211..33716994-chr11:33723846..33727009,3	MCF-7	breast:
2	chr11:33722591..33725977-chr11:33729219..33731745,3	MCF-7	breast:
3	chr11:33724538..33726806-chr11:33736477..33738773,2	MCF-7	breast:
4	chr11:33721709..33724293-chr11:33724908..33726754,2	K562	blood:
5	chr11:33719802..33725980-chr11:33755197..33760109,10	MCF-7	breast:
6	chr11:33720026..33726393-chr11:33756116..33759860,12	MCF-7	breast:
7	chr11:33722219..33726232-chr11:33726761..33732163,6	K562	blood:
8	chr11:33722397..33723935-chr11:33724881..33726688,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C11orf91-1	chr11:33724567-33725791	NONHSAT018710

No data

Variant related genes	Relation type
C11orf91	TF binding region
ENSG00000205177	Chromatin interaction
ENSG00000085063	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11032350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11032363	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11032374	0.85[ASN][1000 genomes]
rs1112840	0.85[ASN][1000 genomes]
rs12360810	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12364970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402953	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1546727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2901375	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181274	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs34944910	0.85[ASN][1000 genomes]
rs35162575	0.85[ASN][1000 genomes]
rs36093484	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4755893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4755894	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56113937	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56399849	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131663	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832113	chr11:33609202-33767781	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1047581	CAPRIN1	cis	cerebellum	SCAN
rs1047581	FSHB	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33718400-33725800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:33722400-33728800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:33722800-33725600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:33722800-33728600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:33722800-33730600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:33723000-33725800	Enhancers	Duodenum Mucosa	Duodenum
7	chr11:33723000-33726000	Enhancers	Fetal Intestine Small	intestine
8	chr11:33723000-33726000	Enhancers	Small Intestine	intestine
9	chr11:33723000-33726400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:33723000-33726400	Enhancers	Fetal Intestine Large	intestine
11	chr11:33723000-33730600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:33723000-33746000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:33723200-33725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:33723200-33725000	Weak transcription	Gastric	stomach
15	chr11:33723200-33725400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:33723200-33726000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:33723200-33726000	Enhancers	HSMM	muscle
18	chr11:33723200-33726400	Enhancers	Colonic Mucosa	Colon
19	chr11:33723200-33726600	Weak transcription	Aorta	Aorta
20	chr11:33723200-33726800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:33723200-33726800	Weak transcription	Ovary	ovary
22	chr11:33723200-33728200	Weak transcription	GM12878-XiMat	blood
23	chr11:33723200-33728400	Enhancers	Brain Angular Gyrus	brain
24	chr11:33723200-33728800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:33723200-33729600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:33723200-33730200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:33723200-33730200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:33723200-33730200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:33723200-33730400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:33723200-33730600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:33723200-33730600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:33723200-33730600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:33723200-33731000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:33723200-33731200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:33723200-33737400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:33723200-33744400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:33723200-33744400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:33723400-33725400	Enhancers	NHLF	lung
39	chr11:33723400-33725600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr11:33723400-33726000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:33723400-33726400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:33723400-33726800	Weak transcription	Primary T cells from cord blood	blood
43	chr11:33723400-33726800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:33723400-33728200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:33723400-33728600	Enhancers	Brain Hippocampus Middle	brain
46	chr11:33723400-33728800	Enhancers	Brain Substantia Nigra	brain
47	chr11:33723400-33729600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:33723400-33730200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:33723400-33730200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:33723400-33731000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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