Variant report

Variant	rs10908463
Chromosome Location	chr1:155286258-155286259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155286084-155286314	K562	blood:	n/a	n/a
2	POLR2A	chr1:155286246-155286267	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:155286174-155286814	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:155285762-155295040	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:155285992-155291727	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:155286102-155287072	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr1:155286105-155286345	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:155286122-155286614	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr1:155285720-155292259	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr1:155286197-155286272	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:155286180-155287212	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:155286092-155286431	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:155285951-155286394	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr1:155286161-155286532	K562	blood:	n/a	n/a
15	POLR2A	chr1:155286219-155286572	K562	blood:	n/a	n/a
16	POLR2A	chr1:155286117-155286629	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155246729..155248789-chr1:155285548..155288546,2	K562	blood:
2	chr1:155247984..155249745-chr1:155285662..155287694,2	MCF-7	breast:

No data

Variant related genes	Relation type
RUSC1	TF binding region
FDPS	TF binding region
ENSG00000176444	Chromatin interaction
ENSG00000143630	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1052176	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1052177	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10796941	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796943	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap]
rs10796945	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap]
rs10908461	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908462	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908465	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs10908469	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11264349	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11264355	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264357	0.83[EUR][1000 genomes]
rs11264358	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264360	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264363	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs11264367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11264369	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11264371	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs11264372	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs11264375	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs12026638	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap]
rs12032720	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041534	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs12044063	0.84[EUR][1000 genomes]
rs12067675	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12079134	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12239114	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap]
rs12724079	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs12724449	0.82[EUR][1000 genomes]
rs12749306	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1360554	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1886905	0.87[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs2071053	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297480	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3020781	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814318	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4620533	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4971072	0.83[ASN][1000 genomes]
rs5005770	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap]
rs6672284	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6677385	0.81[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs6688636	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7524950	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534795	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554780	0.81[EUR][1000 genomes]
rs7556102	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs8177968	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8847	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs932972	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10908463	PKLR	cis	Nerve Tibial	GTEx
rs10908463	GBAP1	cis	Artery Tibial	GTEx
rs10908463	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908463	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908463	GBA	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155280000-155286800	Weak transcription	Brain Anterior Caudate	brain
4	chr1:155280000-155287200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:155280000-155287800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:155280000-155290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:155280000-155290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:155280000-155290200	Weak transcription	Right Atrium	heart
9	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
10	chr1:155280200-155288200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:155280200-155289800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:155280200-155289800	Strong transcription	Fetal Stomach	stomach
13	chr1:155280200-155290000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:155280600-155289800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:155280600-155289800	Weak transcription	Fetal Brain Male	brain
18	chr1:155280600-155290200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:155280600-155290200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:155280800-155290000	Strong transcription	Fetal Thymus	thymus
21	chr1:155280800-155290600	Weak transcription	Small Intestine	intestine
22	chr1:155281200-155289200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:155281400-155288000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:155281400-155290600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:155281600-155287800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:155281600-155290200	Weak transcription	Stomach Mucosa	stomach
27	chr1:155281600-155290600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:155281800-155290000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:155282000-155289600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:155282200-155287600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:155282200-155287800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:155282200-155289800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:155282200-155290200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:155282200-155290600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:155282400-155289000	Strong transcription	HUVEC	blood vessel
36	chr1:155282400-155289200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:155282600-155288200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:155282800-155289800	Strong transcription	Fetal Brain Female	brain
39	chr1:155283000-155288800	Strong transcription	HMEC	breast
40	chr1:155283400-155286600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:155283400-155287800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:155283400-155288000	Weak transcription	Fetal Kidney	kidney
43	chr1:155283400-155288400	Weak transcription	Fetal Lung	lung
44	chr1:155283400-155290200	Weak transcription	Primary B cells from cord blood	blood
45	chr1:155283600-155286600	Weak transcription	A549	lung
46	chr1:155283600-155287200	Weak transcription	Osteobl	bone
47	chr1:155283600-155287800	Weak transcription	Gastric	stomach
48	chr1:155283600-155288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:155283600-155289800	Weak transcription	Fetal Heart	heart
50	chr1:155283600-155289800	Weak transcription	Rectal Smooth Muscle	rectum

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