Variant report

Variant	rs10495774
Chromosome Location	chr2:30506676-30506677
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:30453318..30455814-chr2:30506103..30509890,3	K562	blood:
2	chr2:30492609..30498339-chr2:30504357..30508206,5	K562	blood:
3	chr2:30505644..30508835-chr2:30513800..30516199,3	K562	blood:
4	chr2:30454218..30456365-chr2:30505974..30508839,2	K562	blood:
5	chr2:30502244..30505490-chr2:30505646..30508832,3	K562	blood:
6	chr2:30497560..30499360-chr2:30505202..30507346,2	MCF-7	breast:
7	chr2:30504654..30506690-chr2:30509029..30511575,2	K562	blood:
8	chr2:30505644..30507265-chr2:30513721..30515564,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12469902	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472981	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475240	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396720	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406665	1.00[ASN][1000 genomes]
rs13410030	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17322090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17322097	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs17394102	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787730	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72787734	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787741	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787743	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7569754	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572714	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579019	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7604484	1.00[GIH][hapmap]
rs7606266	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608977	1.00[ASN][1000 genomes]
rs9558	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10495774	TRIM54	cis	cerebellum	SCAN
rs10495774	OTOF	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30487200-30517800	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:30493400-30506800	Weak transcription	Right Ventricle	heart
3	chr2:30494600-30507200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:30496400-30509800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:30496600-30524200	Weak transcription	Right Atrium	heart
6	chr2:30496800-30506800	Weak transcription	Left Ventricle	heart
7	chr2:30497800-30516400	Weak transcription	Gastric	stomach
8	chr2:30499800-30510400	Weak transcription	Aorta	Aorta
9	chr2:30501400-30510800	Enhancers	Primary B cells from cord blood	blood
10	chr2:30501800-30511000	Weak transcription	HSMM	muscle
11	chr2:30502000-30510000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:30502200-30509800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:30503800-30513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:30504600-30510000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:30505800-30510000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:30506000-30509800	Weak transcription	Fetal Thymus	thymus
17	chr2:30506200-30509600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:30506200-30509600	Weak transcription	GM12878-XiMat	blood
19	chr2:30506400-30506800	Weak transcription	Spleen	Spleen
20	chr2:30506400-30507200	Enhancers	K562	blood
21	chr2:30506400-30509600	Weak transcription	Primary T cells from cord blood	blood
22	chr2:30506400-30510000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:30506600-30507000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:30506600-30510000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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