Variant report

Variant	rs10908455
Chromosome Location	chr1:155067283-155067284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155066425..155068289-chr1:155084131..155086403,2	MCF-7	breast:
2	chr1:155066514..155068580-chr1:155068788..155070553,2	MCF-7	breast:
3	chr1:155066957..155067711-chr1:155138966..155139492,2	MCF-7	breast:
4	chr1:155067274..155067813-chr1:155140046..155140799,2	K562	blood:
5	chr1:155062448..155069217-chr1:155142816..155147773,12	MCF-7	breast:
6	chr1:155066781..155067437-chr1:155099017..155099580,2	MCF-7	breast:
7	chr1:155065702..155067995-chr1:155139570..155140962,16	MCF-7	breast:
8	chr1:155065499..155067791-chr1:155070241..155073223,2	MCF-7	breast:
9	chr1:155055416..155060440-chr1:155063419..155068026,8	K562	blood:
10	chr1:155064469..155067923-chr1:155161991..155164572,4	MCF-7	breast:
11	chr1:155066076..155068136-chr1:155139564..155141486,24	MCF-7	breast:
12	chr1:154931783..154934509-chr1:155065563..155068170,2	MCF-7	breast:
13	chr1:155063703..155067297-chr1:155143302..155147272,4	K562	blood:
14	chr1:155066341..155068339-chr1:155131182..155134101,2	MCF-7	breast:
15	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
16	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:
17	chr1:155066527..155067288-chr1:155106043..155106834,2	MCF-7	breast:
18	chr1:155066706..155067679-chr1:155149226..155149765,2	MCF-7	breast:
19	chr1:155066619..155069585-chr1:155195780..155198713,2	K562	blood:
20	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143590	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000202027	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	1.00[ASN][1000 genomes]
rs10796939	0.90[ASN][1000 genomes]
rs10908454	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908456	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264311	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11264312	1.00[ASN][1000 genomes]
rs11264313	0.97[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264321	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264322	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264327	0.93[ASN][1000 genomes]
rs11264328	0.93[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.97[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12145362	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2306124	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	1.00[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4361977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625273	1.00[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	1.00[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	1.00[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7366138	0.95[ASN][1000 genomes]
rs7366355	1.00[ASN][1000 genomes]
rs7367207	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7367758	0.97[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	esv2762194	chr1:155063145-155067283	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10908455	UBE2Q1	cis	cerebellum	SCAN
rs10908455	SMCP	cis	cerebellum	SCAN
rs10908455	APOA1BP	cis	cerebellum	SCAN
rs10908455	SCARNA4	cis	cerebellum	SCAN
rs10908455	RPRD2	cis	parietal	SCAN
rs10908455	SETDB1	cis	parietal	SCAN
rs10908455	ADAM15	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155065200-155067400	Enhancers	Fetal Brain Male	brain
2	chr1:155065600-155067400	Enhancers	Fetal Lung	lung
3	chr1:155065600-155067600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:155065800-155067400	Enhancers	Fetal Muscle Leg	muscle
5	chr1:155065800-155067400	Enhancers	Fetal Stomach	stomach
6	chr1:155065800-155067800	Enhancers	Fetal Heart	heart
7	chr1:155066000-155067400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:155066000-155067600	Enhancers	Liver	Liver
9	chr1:155066200-155067400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:155066200-155067400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:155066200-155067400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:155066200-155067400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:155066200-155067400	Enhancers	Fetal Intestine Small	intestine
14	chr1:155066200-155067600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:155066200-155067600	Enhancers	A549	lung
16	chr1:155066400-155067400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:155066600-155067400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:155066600-155067400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:155066600-155067400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:155066800-155067400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:155067000-155067400	Enhancers	Brain Angular Gyrus	brain
22	chr1:155067000-155067400	Enhancers	Brain Hippocampus Middle	brain
23	chr1:155067000-155067400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:155067000-155067400	Enhancers	Colon Smooth Muscle	Colon
25	chr1:155067000-155067400	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:155067000-155067400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:155067000-155067400	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:155067000-155067600	Enhancers	Brain Substantia Nigra	brain
29	chr1:155067200-155067400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:155067200-155067400	Enhancers	Brain Anterior Caudate	brain
31	chr1:155067200-155067400	Enhancers	HSMMtube	muscle
32	chr1:155067200-155067600	Enhancers	HepG2	liver
33	chr1:155067200-155067800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:155067200-155067800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:155067200-155067800	Enhancers	Brain Cingulate Gyrus	brain
36	chr1:155067200-155074400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:155067200-155075000	Weak transcription	K562	blood

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