Variant report

Variant	rs7552906
Chromosome Location	chr1:151313774-151313775
allele	A/G
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151273432..151279540-chr1:151311017..151317396,9	MCF-7	breast:
2	chr1:151313070..151315906-chr1:234744981..234746645,2	MCF-7	breast:
3	chr1:151272720..151276474-chr1:151311902..151314957,3	K562	blood:
4	chr1:151311947..151315930-chr1:151341715..151344576,4	K562	blood:
5	chr1:151263880..151268121-chr1:151311967..151315494,5	MCF-7	breast:
6	chr1:151313518..151316367-chr1:151341294..151344531,3	MCF-7	breast:
7	chr1:151253109..151257431-chr1:151311446..151315369,6	MCF-7	breast:
8	chr1:151272597..151274611-chr1:151313027..151314093,15	K562	blood:
9	chr1:151313664..151315822-chr1:151337463..151339471,3	MCF-7	breast:
10	chr1:151299980..151303180-chr1:151310152..151314785,6	MCF-7	breast:
11	chr1:151273263..151274229-chr1:151313000..151314268,5	MCF-7	breast:
12	1:151309061-151322694..1:151592347-151603110	GM12878	blood:
13	chr1:151273005..151274023-chr1:151312896..151314194,15	MCF-7	breast:
14	chr1:151312120..151316742-chr1:151370081..151375586,6	MCF-7	breast:
15	chr1:151312109..151317002-chr1:151372398..151376596,7	MCF-7	breast:
16	chr1:151226640..151228529-chr1:151313370..151316215,2	MCF-7	breast:
17	chr1:151312776..151315996-chr1:151344524..151347605,3	MCF-7	breast:
18	chr1:151269975..151273254-chr1:151312272..151315757,4	MCF-7	breast:
19	chr1:151253871..151258133-chr1:151311236..151320814,17	K562	blood:
20	1:151171193-151178589..1:151309061-151322694	Hela-S3	cervix:
21	chr1:151278633..151280248-chr1:151311702..151314022,2	K562	blood:
22	chr1:151313111..151313905-chr1:151371422..151372069,3	MCF-7	breast:
23	chr1:151313762..151315694-chr1:151431128..151433182,2	MCF-7	breast:
24	chr1:151313499..151316475-chr1:151369793..151372161,3	MCF-7	breast:
25	chr1:151262167..151264469-chr1:151313266..151316193,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000206635	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000168264	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000159377	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056847	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]
rs10749660	0.86[JPT][hapmap]
rs10788803	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10788804	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10888408	0.91[JPT][hapmap]
rs10888409	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10888410	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10888411	0.81[ASN][1000 genomes]
rs11204785	0.86[JPT][hapmap]
rs11204791	0.91[JPT][hapmap]
rs11587157	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12069445	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536617	0.82[JPT][hapmap]
rs16827941	0.85[JPT][hapmap]
rs1752387	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs1892196	0.81[JPT][hapmap]
rs2031797	0.82[JPT][hapmap]
rs2275900	0.91[JPT][hapmap]
rs2769267	0.80[GIH][hapmap]
rs2769273	0.80[GIH][hapmap]
rs3811406	0.82[JPT][hapmap]
rs4246525	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]
rs4520422	0.86[JPT][hapmap]
rs4522000	0.86[EUR][1000 genomes]
rs4636463	0.86[JPT][hapmap]
rs4970944	0.86[JPT][hapmap]
rs4970948	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970949	0.87[EUR][1000 genomes]
rs4971013	0.86[JPT][hapmap]
rs4971023	0.86[JPT][hapmap]
rs4971027	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs4971029	0.82[JPT][hapmap]
rs4971030	1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971031	0.86[EUR][1000 genomes]
rs4971032	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971033	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5022636	0.88[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587559	0.86[JPT][hapmap]
rs6587562	0.80[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs6677686	0.88[EUR][1000 genomes]
rs6686402	0.86[JPT][hapmap]
rs6695344	0.82[JPT][hapmap]
rs744536	0.92[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7518924	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7527032	0.86[JPT][hapmap]
rs7531495	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7532935	0.86[JPT][hapmap]
rs7539584	0.86[JPT][hapmap]
rs7544947	0.86[JPT][hapmap]
rs7545392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943637	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	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
6	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7552906	CTSS	cis	cerebellum	SCAN
rs7552906	LCE5A	cis	cerebellum	SCAN
rs7552906	PSMD4	cis	cerebellum	SCAN
rs7552906	HORMAD1	cis	parietal	SCAN
rs7552906	PSMD4	cis	parietal	SCAN
rs7552906	SELENBP1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151301000-151315000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:151301200-151314000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:151301200-151314000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:151301200-151314800	Weak transcription	Fetal Intestine Small	intestine
5	chr1:151301200-151314800	Weak transcription	Gastric	stomach
6	chr1:151301200-151315200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:151301200-151315600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:151301200-151318200	Weak transcription	Right Atrium	heart
9	chr1:151301400-151314800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:151301400-151314800	Weak transcription	Fetal Stomach	stomach
11	chr1:151301400-151316000	Weak transcription	Fetal Kidney	kidney
12	chr1:151306000-151315000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:151308600-151314000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:151309200-151314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:151309200-151314600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:151309600-151314400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:151310200-151314400	Weak transcription	Fetal Brain Female	brain
18	chr1:151311200-151314200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:151311200-151314600	Weak transcription	Spleen	Spleen
20	chr1:151311200-151314800	Weak transcription	Aorta	Aorta
21	chr1:151311400-151314400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:151311600-151314000	Weak transcription	Dnd41	blood
23	chr1:151311600-151314400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:151311600-151314800	Weak transcription	Colonic Mucosa	Colon
25	chr1:151311600-151314800	Weak transcription	Lung	lung
26	chr1:151311600-151314800	Weak transcription	Pancreas	Pancrea
27	chr1:151311600-151315000	Weak transcription	Placenta	Placenta
28	chr1:151311600-151315000	Weak transcription	Right Ventricle	heart
29	chr1:151311800-151314000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:151312200-151314600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:151312200-151314800	Weak transcription	Left Ventricle	heart
32	chr1:151312200-151315000	Weak transcription	Esophagus	oesophagus
33	chr1:151312400-151313800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:151312400-151314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:151312400-151315200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:151312600-151314200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:151312600-151314800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:151312800-151314000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:151313000-151314000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:151313000-151314400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:151313000-151315200	Weak transcription	Ovary	ovary
42	chr1:151313200-151313800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:151313200-151313800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:151313200-151313800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr1:151313200-151313800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:151313200-151313800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr1:151313200-151313800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:151313200-151313800	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr1:151313200-151313800	Enhancers	Primary B cells from peripheral blood	blood
50	chr1:151313200-151313800	Enhancers	Primary hematopoietic stem cells	blood

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