Variant report

Variant	rs12563627
Chromosome Location	chr1:155862966-155862967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:155862449-155863830	SK-N-SH	brain:	n/a	n/a
2	MAFK	chr1:155862598-155862985	IMR90	lung:	n/a	chr1:155862707-155862722
3	MXI1	chr1:155862657-155863757	Hela-S3	cervix:	n/a	n/a
4	JUND	chr1:155862389-155863100	SK-N-SH	brain:	n/a	n/a
5	GTF3C2	chr1:155862413-155862987	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:155862407-155863902	U87	brain:	n/a	n/a
7	POLR2A	chr1:155862565-155863774	Hela-S3	cervix:	n/a	n/a
8	EP300	chr1:155862594-155862976	Hela-S3	cervix:	n/a	n/a
9	MAFK	chr1:155862570-155863801	Hela-S3	cervix:	n/a	chr1:155862707-155862722
10	RFX5	chr1:155862624-155863004	Hela-S3	cervix:	n/a	n/a
11	FOSL2	chr1:155862469-155863055	SK-N-SH	brain:	n/a	n/a
12	FOS	chr1:155862564-155863154	MCF10A-Er-Src	breast:	n/a	n/a
13	FOSL1	chr1:155862303-155863876	HCT-116	colon:	n/a	n/a
14	JUND	chr1:155862452-155863856	HCT-116	colon:	n/a	n/a
15	JUN	chr1:155862553-155863825	Hela-S3	cervix:	n/a	n/a
16	JUND	chr1:155862364-155863901	HCT-116	colon:	n/a	n/a
17	TBP	chr1:155862623-155863031	Hela-S3	cervix:	n/a	n/a
18	JUND	chr1:155862526-155863797	Hela-S3	cervix:	n/a	n/a
19	PBX3	chr1:155862520-155863078	SK-N-SH	brain:	n/a	chr1:155862885-155862896
20	TCF12	chr1:155862374-155863941	SK-N-SH	brain:	n/a	chr1:155863680-155863689
21	POLR2A	chr1:155862401-155863792	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:155862584-155863146	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:155862760-155863729	HUVEC	blood vessel:	n/a	n/a
24	JUND	chr1:155862380-155863812	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr1:155862520-155863890	HUVEC	blood vessel:	n/a	n/a
26	GTF2F1	chr1:155862632-155863109	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr1:155862478-155863117	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr1:155862585-155863840	U87	brain:	n/a	n/a
29	POLR2A	chr1:155862593-155863801	U87	brain:	n/a	n/a
30	TCF12	chr1:155862571-155863055	SK-N-SH	brain:	n/a	n/a
31	TEAD4	chr1:155862415-155863265	ECC-1	luminal epithelium:	n/a	n/a
32	SP1	chr1:155862440-155863041	A549	lung:	n/a	n/a
33	POLR2A	chr1:155862313-155863908	U87	brain:	n/a	n/a
34	MYC	chr1:155862629-155862973	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr1:155862637-155863740	HUVEC	blood vessel:	n/a	n/a
36	FOSL2	chr1:155862445-155862991	A549	lung:	n/a	n/a
37	POLR2A	chr1:155862516-155863843	HUVEC	blood vessel:	n/a	n/a
38	JUN	chr1:155862439-155863895	K562	blood:	n/a	n/a
39	POLR2A	chr1:155862572-155863866	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr1:155862506-155863184	HCT-116	colon:	n/a	n/a
41	PBX3	chr1:155862428-155863130	SK-N-SH	brain:	n/a	chr1:155862885-155862896
42	RCOR1	chr1:155862565-155863114	Hela-S3	cervix:	n/a	n/a
43	BRCA1	chr1:155862690-155863761	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155862181..155863978-chr1:155864920..155867045,2	K562	blood:
2	chr1:155861450..155863047-chr1:155868429..155870558,2	K562	blood:

No data

Variant related genes	Relation type
RNU4-19P	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11264422	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12024880	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12027412	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749405	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1749410	0.87[ASN][1000 genomes]
rs2993207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820594	0.80[JPT][hapmap]
rs4661151	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661175	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs488079	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs490498	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs625658	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs639398	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs656247	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656737	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs670523	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729022	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7517204	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7538214	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822490	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs822504	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs822505	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs822509	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs860295	0.80[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12563627	FAM189B	cis	cerebellum	SCAN
rs12563627	SPRR3	cis	parietal	SCAN
rs12563627	ROBLD3	cis	parietal	SCAN
rs12563627	PRUNE	cis	cerebellum	SCAN
rs12563627	YY1AP1	cis	cerebellum	SCAN
rs12563627	RIT1	cis	cerebellum	SCAN
rs12563627	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12563627	SLC39A1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155831000-155863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
6	chr1:155837600-155863000	Weak transcription	Colonic Mucosa	Colon
7	chr1:155841400-155863000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
9	chr1:155842600-155863400	Weak transcription	Right Atrium	heart
10	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
11	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:155849400-155863000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155851400-155863200	Weak transcription	Aorta	Aorta
15	chr1:155851400-155866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:155851400-155866000	Weak transcription	Spleen	Spleen
17	chr1:155851400-155866400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:155851400-155867400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:155851600-155866800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:155851600-155870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:155852600-155863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:155853000-155863400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:155853200-155863000	Weak transcription	Left Ventricle	heart
24	chr1:155854200-155868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:155854400-155866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:155854400-155866400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:155854800-155868800	Weak transcription	Ovary	ovary
29	chr1:155855200-155863200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:155855800-155863000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:155857000-155863000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:155858600-155864000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:155859000-155864200	Strong transcription	Brain Germinal Matrix	brain
34	chr1:155860000-155864800	Weak transcription	Fetal Stomach	stomach
35	chr1:155860200-155865000	Weak transcription	Fetal Brain Female	brain
36	chr1:155861200-155864200	Enhancers	HepG2	liver
37	chr1:155861400-155866000	Weak transcription	Pancreas	Pancrea
38	chr1:155861600-155866600	Weak transcription	GM12878-XiMat	blood
39	chr1:155861800-155866000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:155862000-155863000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:155862000-155863800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:155862200-155863200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:155862200-155863200	Enhancers	Fetal Kidney	kidney
44	chr1:155862200-155863400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:155862200-155863800	Enhancers	Brain Substantia Nigra	brain
46	chr1:155862200-155864000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:155862200-155864000	Enhancers	Lung	lung
48	chr1:155862200-155864000	Enhancers	NHLF	lung
49	chr1:155862200-155864200	Enhancers	Brain Anterior Caudate	brain
50	chr1:155862200-155864200	Enhancers	HMEC	breast

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