Variant report

Variant	rs56094588
Chromosome Location	chr10:96990806-96990807
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:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:96941976..96944883-chr10:96989765..96992078,3	MCF-7	breast:
2	chr10:96943335..96943883-chr10:96990715..96991433,2	MCF-7	breast:
3	chr10:96989099..96991002-chr10:97047738..97051859,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDLIM1-1	chr10:96990423-96990901	ENSG00000234026
2	lnc-PDLIM1-1	chr10:96990423-96990825	NONHSAT015752
3	lnc-PDLIM1-1	chr10:96990423-96990901	NONHSAT015753
4	lnc-PDLIM1-1	chr10:96990423-96990825	NONHSAT015754

No data

Variant related genes	Relation type
ENSG00000225533	Chromatin interaction
ENSG00000107438	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1032097	1.00[EUR][1000 genomes]
rs1032098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11572073	1.00[EUR][1000 genomes]
rs11572081	1.00[EUR][1000 genomes]
rs11572089	1.00[EUR][1000 genomes]
rs11572132	1.00[EUR][1000 genomes]
rs11572145	1.00[EUR][1000 genomes]
rs11572148	1.00[EUR][1000 genomes]
rs11572176	1.00[EUR][1000 genomes]
rs11812764	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813834	1.00[EUR][1000 genomes]
rs11814600	1.00[EUR][1000 genomes]
rs11815378	1.00[EUR][1000 genomes]
rs11816316	1.00[EUR][1000 genomes]
rs11816732	1.00[EUR][1000 genomes]
rs11817176	1.00[EUR][1000 genomes]
rs11817388	1.00[EUR][1000 genomes]
rs11818486	1.00[EUR][1000 genomes]
rs11819238	1.00[EUR][1000 genomes]
rs2094293	1.00[EUR][1000 genomes]
rs2094294	1.00[EUR][1000 genomes]
rs2860950	1.00[EUR][1000 genomes]
rs2860951	1.00[EUR][1000 genomes]
rs45454292	1.00[EUR][1000 genomes]
rs45487391	1.00[EUR][1000 genomes]
rs45491002	1.00[EUR][1000 genomes]
rs45495404	1.00[EUR][1000 genomes]
rs45620737	1.00[EUR][1000 genomes]
rs55700247	1.00[EUR][1000 genomes]
rs55740007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55786415	1.00[EUR][1000 genomes]
rs55915838	1.00[EUR][1000 genomes]
rs55937167	1.00[EUR][1000 genomes]
rs56187632	1.00[EUR][1000 genomes]
rs56264187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56412102	1.00[EUR][1000 genomes]
rs56979418	1.00[EUR][1000 genomes]
rs56999073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58894719	1.00[EUR][1000 genomes]
rs59277980	1.00[EUR][1000 genomes]
rs59282006	1.00[EUR][1000 genomes]
rs59329992	1.00[EUR][1000 genomes]
rs59485845	1.00[EUR][1000 genomes]
rs60480656	1.00[EUR][1000 genomes]
rs60916665	1.00[EUR][1000 genomes]
rs61478963	1.00[EUR][1000 genomes]
rs61634481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6583982	1.00[EUR][1000 genomes]
rs6583986	1.00[EUR][1000 genomes]
rs7070484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7074994	1.00[EUR][1000 genomes]
rs7078505	1.00[EUR][1000 genomes]
rs7083576	1.00[EUR][1000 genomes]
rs7083837	1.00[EUR][1000 genomes]
rs7084045	1.00[EUR][1000 genomes]
rs7085646	1.00[EUR][1000 genomes]
rs7087494	1.00[EUR][1000 genomes]
rs7088962	1.00[EUR][1000 genomes]
rs7090248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7090669	1.00[EUR][1000 genomes]
rs7090961	1.00[EUR][1000 genomes]
rs7091711	1.00[EUR][1000 genomes]
rs7093626	1.00[EUR][1000 genomes]
rs7100479	1.00[EUR][1000 genomes]
rs74150750	1.00[EUR][1000 genomes]
rs74150764	1.00[EUR][1000 genomes]
rs74150766	1.00[EUR][1000 genomes]
rs74150767	1.00[EUR][1000 genomes]
rs74150768	1.00[EUR][1000 genomes]
rs74150772	1.00[EUR][1000 genomes]
rs74150780	1.00[EUR][1000 genomes]
rs74150781	1.00[EUR][1000 genomes]
rs74150782	1.00[EUR][1000 genomes]
rs74150785	1.00[EUR][1000 genomes]
rs74150786	1.00[EUR][1000 genomes]
rs74150790	1.00[EUR][1000 genomes]
rs74150792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74150793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74150795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7894207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7915255	1.00[EUR][1000 genomes]
rs7918727	1.00[EUR][1000 genomes]
rs7918803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7919415	1.00[EUR][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96970200-96992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:96987800-96991000	Enhancers	HMEC	breast
3	chr10:96989200-96991000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:96989600-96991000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr10:96989600-96991000	Active TSS	Brain Anterior Caudate	brain
6	chr10:96989600-96991000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr10:96989600-96991200	Active TSS	Brain Angular Gyrus	brain
8	chr10:96989800-96991000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:96989800-96991000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:96989800-96991000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr10:96989800-96991000	Active TSS	Brain Cingulate Gyrus	brain
12	chr10:96989800-96991000	Active TSS	Brain Germinal Matrix	brain
13	chr10:96989800-96991000	Active TSS	Fetal Brain Female	brain
14	chr10:96989800-96991600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr10:96990000-96991000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:96990000-96991000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:96990000-96991000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr10:96990000-96991000	Flanking Active TSS	GM12878-XiMat	blood
19	chr10:96990000-96991200	Active TSS	Fetal Kidney	kidney
20	chr10:96990000-96991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr10:96990000-96991400	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr10:96990000-96991600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr10:96990000-96995400	Weak transcription	K562	blood
24	chr10:96990000-96995800	Weak transcription	HepG2	liver
25	chr10:96990200-96991000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:96990200-96991000	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr10:96990200-96991000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr10:96990200-96991000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:96990200-96991000	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr10:96990200-96991000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr10:96990200-96991000	Active TSS	Brain Hippocampus Middle	brain
32	chr10:96990200-96991000	Active TSS	Brain Substantia Nigra	brain
33	chr10:96990200-96991000	Active TSS	Colon Smooth Muscle	Colon
34	chr10:96990200-96991000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr10:96990200-96991000	Active TSS	Fetal Intestine Small	intestine
36	chr10:96990200-96991000	Active TSS	Fetal Lung	lung
37	chr10:96990200-96991000	Flanking Active TSS	Pancreas	Pancrea
38	chr10:96990200-96991000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr10:96990200-96991400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr10:96990200-96991600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:96990400-96991000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
42	chr10:96990400-96991000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:96990400-96991000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr10:96990400-96991000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:96990400-96991000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr10:96990400-96991000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr10:96990400-96991000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr10:96990400-96991000	Active TSS	Primary T cells from cord blood	blood
49	chr10:96990400-96991000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
50	chr10:96990400-96991000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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