Variant report

Variant	rs488079
Chromosome Location	chr1:155890581-155890582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155890253-155891525	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:155890242-155890974	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:155890287-155891336	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:155890296-155890910	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:155890287-155891395	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:155890137-155891497	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:155890248-155891268	K562	blood:	n/a	n/a
8	POLR2A	chr1:155890498-155890987	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:155890285-155891040	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:155890297-155890854	HL-60	blood:	n/a	n/a
11	POLR2A	chr1:155890554-155890817	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:155890234-155891858	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr1:155890414-155891143	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr1:155890206-155891516	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr1:155890411-155890602	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:155890156-155890721	K562	blood:	n/a	n/a
17	POLR2A	chr1:155890420-155891083	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:155890344-155890632	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:155890310-155890587	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:155890134-155891462	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:155890342-155891264	K562	blood:	n/a	n/a
22	POLR2A	chr1:155889675-155892623	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:155890354-155891000	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155889116..155891316-chr1:155948021..155950216,2	K562	blood:

No data

Variant related genes	Relation type
SNORA42	TF binding region
KIAA0907	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000273002	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796955	0.80[CHB][hapmap]
rs11264422	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12024880	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027412	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563627	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]
rs1749405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1749410	0.82[ASN][1000 genomes]
rs1889532	0.80[CHB][hapmap]
rs2993207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820594	0.80[JPT][hapmap]
rs4661151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661175	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661218	0.80[CHB][hapmap]
rs490498	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639398	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656737	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670523	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs729022	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7517204	0.82[ASN][1000 genomes]
rs7538214	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs822490	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs822504	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822505	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs822509	0.82[ASN][1000 genomes]
rs860295	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs928596	0.80[CHB][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs488079	RIT1	cis	cerebellum	SCAN
rs488079	FAM189B	cis	cerebellum	SCAN
rs488079	SPRR3	cis	parietal	SCAN
rs488079	PRUNE	cis	cerebellum	SCAN
rs488079	ROBLD3	cis	parietal	SCAN
rs488079	SLC39A1	cis	cerebellum	SCAN
rs488079	YY1AP1	cis	cerebellum	SCAN
rs488079	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs488079	UBQLN4	trans	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155881600-155890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155881800-155893600	Strong transcription	HMEC	breast
3	chr1:155881800-155898800	Strong transcription	HUVEC	blood vessel
4	chr1:155881800-155899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:155881800-155900600	Strong transcription	Fetal Muscle Leg	muscle
6	chr1:155881800-155901200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:155881800-155901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:155882000-155898800	Strong transcription	NH-A	brain
9	chr1:155882000-155899400	Strong transcription	Fetal Intestine Large	intestine
10	chr1:155882000-155899800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:155882000-155900000	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:155882000-155900000	Strong transcription	Liver	Liver
13	chr1:155882000-155900200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:155882000-155900400	Strong transcription	Primary B cells from cord blood	blood
15	chr1:155882000-155900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:155882000-155900600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:155882000-155900600	Strong transcription	Placenta	Placenta
18	chr1:155882000-155900600	Strong transcription	Fetal Stomach	stomach
19	chr1:155882000-155900600	Strong transcription	Left Ventricle	heart
20	chr1:155882000-155900800	Strong transcription	Thymus	Thymus
21	chr1:155882000-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:155882000-155901400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:155882000-155901400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:155882200-155898600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:155882200-155900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:155882200-155900600	Strong transcription	Fetal Thymus	thymus
27	chr1:155882200-155901000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:155882200-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:155882200-155901200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:155882200-155901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:155882200-155901400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:155882200-155901400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:155882200-155903000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:155882400-155893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:155882400-155898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:155882400-155900000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:155882400-155900000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:155882400-155900000	Strong transcription	Adipose Nuclei	Adipose
39	chr1:155882400-155900200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:155882600-155898800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:155882600-155899000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:155882600-155899000	Strong transcription	NHEK	skin
43	chr1:155882600-155900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:155882600-155900200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:155882600-155901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:155882600-155901600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:155882800-155897400	Strong transcription	Fetal Brain Female	brain
48	chr1:155882800-155897400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:155882800-155897800	Strong transcription	A549	lung
50	chr1:155882800-155899400	Strong transcription	Muscle Satellite Cultured Cells	--

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