Variant report

Variant	rs1056847
Chromosome Location	chr1:151288172-151288173
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151286040..151288364-chr1:151291772..151293505,2	MCF-7	breast:
2	chr1:151287266..151289883-chr1:151318001..151320397,2	K562	blood:
3	1:151283078-151288777..1:151516085-151535167	GM12878	blood:
4	1:151283078-151288777..1:151333184-151350267	GM12878	blood:
5	chr1:151279180..151282916-chr1:151286769..151288815,3	MCF-7	breast:
6	1:151246650-151254384..1:151283078-151288777	Hela-S3	cervix:
7	1:151219411-151234038..1:151283078-151288777	Hela-S3	cervix:
8	1:151254384-151268403..1:151283078-151288777	Hela-S3	cervix:
9	chr1:151281649..151290428-chr1:151296694..151302315,21	MCF-7	breast:
10	1:151283078-151288777..1:151411623-151426875	Hela-S3	cervix:
11	1:151283078-151288777..1:151618750-151636526	GM12878	blood:
12	chr1:151287182..151288727-chr1:151317734..151320228,2	MCF-7	breast:
13	1:151283078-151288777..1:151368336-151375897	GM12878	blood:
14	chr1:151277709..151281800-chr1:151286045..151289490,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232671	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000223861	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10749660	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10788801	0.86[JPT][hapmap]
rs10788803	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10788804	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10888408	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10888409	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10888410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888411	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204785	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11204791	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11204795	0.89[EUR][1000 genomes]
rs11587157	0.80[EUR][1000 genomes]
rs12069445	0.81[EUR][1000 genomes]
rs1536617	0.90[JPT][hapmap]
rs16827941	0.95[JPT][hapmap]
rs1752387	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs1892196	0.83[GIH][hapmap];0.81[JPT][hapmap]
rs2025900	0.81[JPT][hapmap]
rs2031797	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs2275900	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2769268	0.81[JPT][hapmap]
rs2769273	0.81[JPT][hapmap]
rs2800946	0.81[JPT][hapmap]
rs3811405	0.86[JPT][hapmap]
rs3811406	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4246525	0.91[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4520422	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs4522000	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4636463	0.90[JPT][hapmap]
rs4970944	0.95[JPT][hapmap]
rs4970948	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970949	0.81[EUR][1000 genomes]
rs4971013	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs4971023	0.95[JPT][hapmap]
rs4971027	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4971029	0.90[JPT][hapmap]
rs4971030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971031	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971032	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971033	0.87[EUR][1000 genomes]
rs5022636	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587559	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6587562	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs6677686	0.81[EUR][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6686402	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs6695344	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs744536	0.91[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7518924	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7527032	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7531495	0.83[EUR][1000 genomes]
rs7532935	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7539584	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7544947	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs7545392	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7552906	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs943637	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1056847	LCE5A	cis	cerebellum	SCAN
rs1056847	CTSS	cis	cerebellum	SCAN
rs1056847	PSMD4	cis	parietal	SCAN
rs1056847	HIST2H2AC	cis	parietal	SCAN
rs1056847	SELENBP1	cis	cerebellum	SCAN
rs1056847	PSMD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151257200-151297600	Strong transcription	Dnd41	blood
2	chr1:151257600-151293600	Strong transcription	Brain Germinal Matrix	brain
3	chr1:151258200-151297200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr1:151258400-151293400	Strong transcription	Fetal Brain Female	brain
5	chr1:151258400-151297800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:151260000-151298000	Strong transcription	Thymus	Thymus
7	chr1:151261600-151297800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:151262000-151298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:151262600-151297600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:151265800-151298000	Strong transcription	Fetal Thymus	thymus
11	chr1:151270600-151289400	Strong transcription	GM12878-XiMat	blood
12	chr1:151271400-151298800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:151273200-151298000	Strong transcription	Primary T cells from cord blood	blood
14	chr1:151273800-151297800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:151274400-151295000	Strong transcription	Primary B cells from cord blood	blood
16	chr1:151274600-151288800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr1:151280200-151299200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:151280400-151299000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:151281400-151288400	Genic enhancers	Fetal Muscle Leg	muscle
20	chr1:151281800-151288200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:151281800-151288400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:151281800-151288600	Enhancers	Right Atrium	heart
23	chr1:151282400-151289000	Genic enhancers	Placenta	Placenta
24	chr1:151283200-151288200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:151283200-151288800	Genic enhancers	Hela-S3	cervix
26	chr1:151283200-151298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:151283200-151299000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:151283400-151296000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:151283400-151297400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:151283600-151288200	Strong transcription	Fetal Kidney	kidney
31	chr1:151283600-151289200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:151283600-151289200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:151283800-151289000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:151283800-151289200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:151284600-151288400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:151284600-151292400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:151284800-151288600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:151284800-151289000	Strong transcription	Aorta	Aorta
39	chr1:151284800-151292800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:151284800-151295200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:151285000-151288800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:151285000-151289600	Strong transcription	HepG2	liver
43	chr1:151285000-151297200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:151285200-151288600	Genic enhancers	Adipose Nuclei	Adipose
45	chr1:151285200-151289000	Genic enhancers	Right Ventricle	heart
46	chr1:151285200-151291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:151285200-151295400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:151285200-151297400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:151285400-151294400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:151285600-151289200	Strong transcription	H1 Cell Line	embryonic stem cell

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