Variant report

Variant	rs10528
Chromosome Location	chr2:54889149-54889150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:1)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54888467-54889467	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:54889058-54889281	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54790164..54792599-chr2:54886849..54889331,2	K562	blood:
2	chr2:54887215..54889644-chr2:55458708..55461317,2	MCF-7	breast:

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	SPTBN1	hsa-miR-93-5p	chr2:54889148-54889170

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
SPTBN1	miRNA target site

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10170355	0.88[CHB][hapmap]
rs10176359	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs10176445	0.88[CHB][hapmap]
rs10182836	0.88[CHB][hapmap]
rs10183043	0.85[EUR][1000 genomes]
rs10183867	0.88[CHB][hapmap]
rs10184128	0.88[CHB][hapmap]
rs10188185	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs10193692	0.86[CHB][hapmap]
rs10205410	0.84[CHB][hapmap]
rs10206143	0.88[CHB][hapmap]
rs10210502	0.87[EUR][1000 genomes]
rs1137645	0.88[CHB][hapmap]
rs11555856	0.87[EUR][1000 genomes]
rs11892236	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11892443	0.86[CHB][hapmap]
rs11892703	0.85[ASN][1000 genomes]
rs11896957	0.91[EUR][1000 genomes]
rs11902659	0.91[EUR][1000 genomes]
rs11902987	0.88[CHB][hapmap]
rs11904679	1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12713262	0.84[EUR][1000 genomes]
rs12713263	0.84[EUR][1000 genomes]
rs12713264	0.88[CHB][hapmap]
rs12713265	0.88[CHB][hapmap]
rs12713268	0.88[CHB][hapmap]
rs12713269	0.88[CHB][hapmap]
rs12713270	0.87[EUR][1000 genomes]
rs12713271	0.87[EUR][1000 genomes]
rs12713272	0.91[EUR][1000 genomes]
rs12713273	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs12987967	0.87[EUR][1000 genomes]
rs13004944	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13021606	0.91[EUR][1000 genomes]
rs13021615	0.85[EUR][1000 genomes]
rs13386146	0.88[CHB][hapmap]
rs13391522	0.88[CHB][hapmap]
rs13391803	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs13399656	1.00[CHB][hapmap]
rs13403284	0.88[CHB][hapmap]
rs13408295	0.85[EUR][1000 genomes]
rs17039558	0.84[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17045939	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs17046036	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17046061	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17046067	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17046077	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17046097	0.88[CHB][hapmap]
rs17046108	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17046257	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs2048370	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2229503	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2271329	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3287	0.88[CHB][hapmap]
rs34077590	0.90[EUR][1000 genomes]
rs34094680	0.90[EUR][1000 genomes]
rs34263579	0.81[EUR][1000 genomes]
rs34308676	0.86[EUR][1000 genomes]
rs34311770	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34978408	0.90[EUR][1000 genomes]
rs35619551	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36018286	0.81[EUR][1000 genomes]
rs3739109	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3796019	0.88[CHB][hapmap]
rs3796022	0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs3850350	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4261758	0.84[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4319969	0.80[EUR][1000 genomes]
rs4346422	0.88[CHB][hapmap]
rs4358162	0.87[EUR][1000 genomes]
rs4455200	0.86[CHB][hapmap]
rs4519566	0.89[EUR][1000 genomes]
rs4577321	0.89[EUR][1000 genomes]
rs57281248	0.90[EUR][1000 genomes]
rs58419243	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61126015	0.85[EUR][1000 genomes]
rs6545430	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs6545435	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs66693131	0.83[EUR][1000 genomes]
rs6706263	0.86[CHB][hapmap]
rs67079536	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6721612	0.91[EUR][1000 genomes]
rs6724136	0.85[EUR][1000 genomes]
rs67244067	0.86[EUR][1000 genomes]
rs67246257	0.82[ASN][1000 genomes]
rs6730876	0.91[EUR][1000 genomes]
rs6734445	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs6734536	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes]
rs6741053	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67514855	0.82[ASN][1000 genomes]
rs67617923	0.82[ASN][1000 genomes]
rs72806653	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72806698	0.82[ASN][1000 genomes]
rs7340302	0.88[CHB][hapmap]
rs7424459	0.91[EUR][1000 genomes]
rs7556752	0.88[CHB][hapmap]
rs7569127	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs7584223	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs7586066	0.93[EUR][1000 genomes]
rs7599241	0.88[CHB][hapmap]
rs7602992	0.84[EUR][1000 genomes]
rs7608414	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10528	RPL23AP32	cis	cerebellum	SCAN
rs10528	VRK2	cis	cerebellum	SCAN
rs10528	EML6	cis	Thyroid	GTEx
rs10528	C2orf63	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:54846600-54898000	Strong transcription	Dnd41	blood
8	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:54848600-54892400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:54862200-54896600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr2:54862400-54892800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:54862600-54892400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:54862600-54892400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:54862600-54893400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:54863000-54892000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:54863000-54892200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:54863000-54892400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:54863000-54895000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
23	chr2:54863600-54897000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:54864200-54893600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:54865400-54892800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:54866000-54892800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:54866400-54892400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:54866400-54897200	Strong transcription	Primary B cells from cord blood	blood
33	chr2:54867200-54892200	Strong transcription	HSMMtube	muscle
34	chr2:54867200-54892400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:54867200-54892400	Strong transcription	NHEK	skin
36	chr2:54867200-54892800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:54867200-54892800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:54867200-54897800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:54867200-54898200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:54868400-54892400	Strong transcription	Fetal Intestine Large	intestine
41	chr2:54868800-54898600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:54869000-54892000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:54869000-54896400	Strong transcription	Colonic Mucosa	Colon
44	chr2:54869400-54892000	Strong transcription	Fetal Lung	lung
45	chr2:54869600-54893400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:54869600-54898600	Strong transcription	Fetal Thymus	thymus
47	chr2:54869800-54890200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:54869800-54891400	Strong transcription	Placenta	Placenta
49	chr2:54869800-54891800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr2:54869800-54895200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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