Variant report

Variant	rs4246525
Chromosome Location	chr1:151257739-151257740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151257292-151257867	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151253853..151259248-chr1:151295350..151301325,11	K562	blood:
2	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
3	chr1:151161155..151162888-chr1:151254618..151258389,3	MCF-7	breast:
4	chr1:151252184..151258894-chr1:151295105..151301119,15	MCF-7	breast:
5	1:151254384-151268403..1:151402394-151411623	GM12878	blood:
6	chr1:151253871..151258133-chr1:151311236..151320814,17	K562	blood:
7	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
8	chr1:151257337..151259306-chr1:151293938..151295656,2	K562	blood:
9	chr1:151226153..151228488-chr1:151257371..151260075,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF687	TF binding region
ENSG00000232671	TF binding region
ENSG00000238711	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143390	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1056847	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]
rs10749660	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs10788801	0.81[JPT][hapmap]
rs10788803	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788804	0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap]
rs10888408	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs10888409	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888410	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888411	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204785	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs11204791	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs11204795	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12048670	0.84[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs2031797	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs2275900	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs3811405	0.81[JPT][hapmap]
rs3811406	0.86[GIH][hapmap];0.85[JPT][hapmap]
rs41302131	0.84[ASN][1000 genomes]
rs4520422	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4522000	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4636463	0.85[JPT][hapmap]
rs4970944	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4970948	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971013	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4971023	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4971025	0.84[ASN][1000 genomes]
rs4971026	0.84[ASN][1000 genomes]
rs4971027	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971031	0.85[EUR][1000 genomes]
rs4971032	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5022636	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587559	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs6587562	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6678528	0.81[JPT][hapmap]
rs6681071	0.82[ASN][1000 genomes]
rs6681163	0.82[ASN][1000 genomes]
rs6686402	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs6695344	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs744536	0.83[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap]
rs7518924	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7527032	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs7532935	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs7539584	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs7544947	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs7545392	0.91[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs7552906	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs943637	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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 target site	106 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4246525	SELENBP1	cis	cerebellum	SCAN
rs4246525	LCE5A	cis	cerebellum	SCAN
rs4246525	CTSS	cis	cerebellum	SCAN
rs4246525	PSMD4	cis	parietal	SCAN
rs4246525	PSMD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151255800-151258800	Weak transcription	Aorta	Aorta
2	chr1:151256000-151261000	Weak transcription	Fetal Kidney	kidney
3	chr1:151256000-151270600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:151256400-151258600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:151256400-151258600	Weak transcription	HUVEC	blood vessel
6	chr1:151256600-151258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:151256600-151258600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:151256600-151258600	Weak transcription	Liver	Liver
9	chr1:151256600-151258600	Weak transcription	Ovary	ovary
10	chr1:151256600-151258600	Weak transcription	A549	lung
11	chr1:151256800-151258200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151256800-151258200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:151256800-151258200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:151256800-151258400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:151256800-151258400	Weak transcription	Fetal Brain Female	brain
16	chr1:151256800-151258400	Weak transcription	HSMMtube	muscle
17	chr1:151256800-151258600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:151256800-151258600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:151256800-151258600	Weak transcription	NH-A	brain
20	chr1:151256800-151258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:151256800-151258800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:151256800-151258800	Weak transcription	Esophagus	oesophagus
23	chr1:151256800-151258800	Weak transcription	NHLF	lung
24	chr1:151256800-151259000	Weak transcription	Small Intestine	intestine
25	chr1:151256800-151261600	Weak transcription	Psoas Muscle	Psoas
26	chr1:151256800-151264600	Weak transcription	NHDF-Ad	bronchial
27	chr1:151256800-151268400	Strong transcription	NHEK	skin
28	chr1:151256800-151281400	Strong transcription	Fetal Stomach	stomach
29	chr1:151257000-151257800	Genic enhancers	Primary B cells from cord blood	blood
30	chr1:151257000-151257800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:151257000-151258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:151257000-151258400	Weak transcription	Colonic Mucosa	Colon
33	chr1:151257000-151258400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:151257000-151258600	Weak transcription	Hela-S3	cervix
35	chr1:151257000-151258800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:151257000-151258800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:151257000-151259000	Weak transcription	Brain Anterior Caudate	brain
38	chr1:151257000-151259600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:151257000-151259600	Strong transcription	Thymus	Thymus
40	chr1:151257000-151260600	Weak transcription	Stomach Mucosa	stomach
41	chr1:151257000-151261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:151257000-151266400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:151257000-151266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:151257000-151266600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:151257000-151267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:151257000-151281200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:151257000-151281800	Weak transcription	Right Atrium	heart
48	chr1:151257200-151257800	Genic enhancers	GM12878-XiMat	blood
49	chr1:151257200-151258000	Weak transcription	Lung	lung
50	chr1:151257200-151258200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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