Variant report

Variant	rs256962
Chromosome Location	chr5:114942711-114942712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr5:114942259-114942726	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:114938174..114939846-chr5:114942589..114944431,2	K562	blood:
2	chr5:114934250..114936093-chr5:114941092..114942888,2	MCF-7	breast:
3	chr5:114941287..114943087-chr5:114960298..114961857,2	MCF-7	breast:
4	chr5:114936292..114939674-chr5:114939747..114944089,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-8	chr5:114942511-114942929	ncRnaDb_ncrna_FR309745_1

No data

Variant related genes	Relation type
TICAM2	TF binding region
ENSG00000249249	Chromatin interaction
ENSG00000251201	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000243414	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10055677	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13164545	0.80[CHB][hapmap]
rs13186296	0.90[ASN][1000 genomes]
rs171773	0.83[EUR][1000 genomes]
rs2303747	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2546487	0.83[MEX][hapmap]
rs2559990	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256941	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256942	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs256943	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256945	0.81[CEU][hapmap]
rs256947	0.94[ASN][1000 genomes]
rs256948	0.94[ASN][1000 genomes]
rs256949	0.93[ASN][1000 genomes]
rs256950	0.94[ASN][1000 genomes]
rs256951	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256952	0.94[ASN][1000 genomes]
rs256953	0.94[ASN][1000 genomes]
rs256954	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256955	0.87[CHB][hapmap]
rs256959	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs256964	0.82[AMR][1000 genomes]
rs256968	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256976	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs256994	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256996	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs377290	0.99[ASN][1000 genomes]
rs3822579	0.91[ASN][1000 genomes]
rs387718	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs400570	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs413059	0.98[ASN][1000 genomes]
rs416234	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424434	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428191	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62371215	0.82[ASN][1000 genomes]
rs698365	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs698366	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs698367	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs712550	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712551	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7702283	0.94[ASN][1000 genomes]
rs7702869	0.93[ASN][1000 genomes]
rs7702881	0.93[ASN][1000 genomes]
rs790824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790825	0.97[ASN][1000 genomes]
rs9326969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs256962	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114937800-114951600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:114938200-114944400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:114938200-114957200	Weak transcription	Small Intestine	intestine
4	chr5:114938200-114958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:114938200-114960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:114938400-114944000	Strong transcription	Dnd41	blood
7	chr5:114938400-114951400	Weak transcription	HepG2	liver
8	chr5:114938600-114943200	Weak transcription	Placenta	Placenta
9	chr5:114938600-114943600	Weak transcription	Left Ventricle	heart
10	chr5:114938600-114943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:114938600-114944000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:114938600-114944400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:114938600-114948400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:114938600-114949600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:114938600-114949600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:114938600-114949800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:114938600-114950000	Weak transcription	Fetal Intestine Large	intestine
18	chr5:114938600-114950000	Weak transcription	HSMMtube	muscle
19	chr5:114938600-114950200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:114938600-114951600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:114938600-114951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:114938600-114951800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:114938600-114951800	Weak transcription	Esophagus	oesophagus
24	chr5:114938600-114958000	Weak transcription	Ovary	ovary
25	chr5:114938600-114960000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:114938800-114943600	Weak transcription	Psoas Muscle	Psoas
27	chr5:114938800-114943800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:114938800-114945600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:114938800-114946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:114938800-114947600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:114938800-114948400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:114938800-114948400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:114938800-114949600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:114938800-114949600	Weak transcription	Hela-S3	cervix
35	chr5:114938800-114950000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:114938800-114950200	Weak transcription	Primary T cells from cord blood	blood
37	chr5:114938800-114951600	Weak transcription	K562	blood
38	chr5:114938800-114951800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:114938800-114951800	Weak transcription	Thymus	Thymus
40	chr5:114938800-114951800	Weak transcription	NHLF	lung
41	chr5:114938800-114952000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:114938800-114953800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:114938800-114954000	Weak transcription	Fetal Brain Female	brain
44	chr5:114938800-114954200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:114938800-114954200	Weak transcription	Colonic Mucosa	Colon
46	chr5:114938800-114957400	Weak transcription	Aorta	Aorta
47	chr5:114938800-114958600	Weak transcription	Right Ventricle	heart
48	chr5:114938800-114960000	Weak transcription	Lung	lung
49	chr5:114939000-114943600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:114939000-114943800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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