Variant report

Variant	rs10888409
Chromosome Location	chr1:151271782-151271783
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151266126..151269327-chr1:151270044..151271811,3	MCF-7	breast:
2	chr1:151270824..151272634-chr1:151430532..151433338,2	MCF-7	breast:
3	1:151171193-151178589..1:151270864-151283078	K562	blood:
4	chr1:151270481..151273348-chr1:151299079..151301611,3	MCF-7	breast:
5	chr1:151269975..151273254-chr1:151312272..151315757,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273481	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143393	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1056847	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]
rs10749660	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10788801	0.86[JPT][hapmap]
rs10788803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10788804	0.96[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs10888408	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10888410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888411	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204785	0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11204791	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11204795	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12048670	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1536617	0.91[JPT][hapmap]
rs16827941	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs1752387	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs1892196	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.86[GIH][hapmap];0.91[JPT][hapmap]
rs2275900	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2769268	0.82[JPT][hapmap]
rs2769273	0.82[JPT][hapmap]
rs2800946	0.82[JPT][hapmap]
rs3811405	0.86[JPT][hapmap]
rs3811406	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs41302131	0.86[ASN][1000 genomes]
rs4246525	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]
rs4520422	0.84[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs4522000	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4636463	0.90[JPT][hapmap]
rs4970944	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs4970948	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971013	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs4971023	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4971025	0.86[ASN][1000 genomes]
rs4971026	0.86[ASN][1000 genomes]
rs4971027	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971029	0.91[JPT][hapmap]
rs4971030	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971031	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971032	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971033	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5022636	0.88[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587559	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6587562	0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6681071	0.85[ASN][1000 genomes]
rs6681163	0.85[ASN][1000 genomes]
rs6686402	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs6695344	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap]
rs744536	0.92[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs7518924	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527032	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7531495	0.81[EUR][1000 genomes]
rs7532935	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7539584	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7544947	0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs7545392	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552906	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]
rs943637	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10888409	LCE5A	cis	cerebellum	SCAN
rs10888409	SELENBP1	cis	cerebellum	SCAN
rs10888409	HIST2H2AC	cis	parietal	SCAN
rs10888409	PSMD4	cis	cerebellum	SCAN
rs10888409	PSMD4	cis	parietal	SCAN
rs10888409	CTSS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151256800-151281400	Strong transcription	Fetal Stomach	stomach
2	chr1:151257000-151281200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:151257000-151281800	Weak transcription	Right Atrium	heart
4	chr1:151257200-151283000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:151257200-151297600	Strong transcription	Dnd41	blood
6	chr1:151257400-151272200	Strong transcription	HepG2	liver
7	chr1:151257400-151281200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:151257400-151281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:151257400-151281800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:151257400-151282000	Strong transcription	Fetal Lung	lung
11	chr1:151257400-151282200	Strong transcription	Fetal Intestine Large	intestine
12	chr1:151257400-151282200	Strong transcription	Osteobl	bone
13	chr1:151257400-151283600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr1:151257600-151272200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:151257600-151281200	Strong transcription	Adipose Nuclei	Adipose
16	chr1:151257600-151281200	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:151257600-151293600	Strong transcription	Brain Germinal Matrix	brain
18	chr1:151257800-151281600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:151257800-151282000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:151258000-151283200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:151258000-151283600	Strong transcription	Lung	lung
22	chr1:151258200-151271800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr1:151258200-151271800	Strong transcription	Gastric	stomach
24	chr1:151258200-151281400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:151258200-151281600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:151258200-151282000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:151258200-151297200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:151258400-151271800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:151258400-151272000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:151258400-151281000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151258400-151281800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr1:151258400-151283000	Strong transcription	Colonic Mucosa	Colon
33	chr1:151258400-151293400	Strong transcription	Fetal Brain Female	brain
34	chr1:151258400-151297800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:151258600-151272000	Strong transcription	Ovary	ovary
36	chr1:151258600-151272200	Strong transcription	Colon Smooth Muscle	Colon
37	chr1:151258600-151276400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:151258600-151282000	Strong transcription	Liver	Liver
39	chr1:151258600-151282000	Strong transcription	Left Ventricle	heart
40	chr1:151258800-151271800	Strong transcription	Aorta	Aorta
41	chr1:151258800-151271800	Strong transcription	Esophagus	oesophagus
42	chr1:151258800-151281400	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr1:151258800-151281600	Strong transcription	NHLF	lung
44	chr1:151259600-151281800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:151260000-151298000	Strong transcription	Thymus	Thymus
46	chr1:151260400-151281200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:151261600-151283400	Strong transcription	Spleen	Spleen
48	chr1:151261600-151297800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:151261800-151272000	Strong transcription	Right Ventricle	heart
50	chr1:151262000-151298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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