Variant report

Variant	rs9326969
Chromosome Location	chr5:114957561-114957562
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114934797..114939548-chr5:114953575..114961976,8	K562	blood:
2	chr5:114945298..114947045-chr5:114956515..114958044,2	K562	blood:
3	chr5:114950269..114954273-chr5:114956632..114959836,4	MCF-7	breast:
4	chr5:114955799..114957829-chr5:115169410..115172369,2	K562	blood:
5	chr5:114949905..114952217-chr5:114956239..114958053,2	K562	blood:

Variant related genes	Relation type
ENSG00000249249	Chromatin interaction
ENSG00000145782	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000251201	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];0.95[ASN][1000 genomes]
rs13164545	0.80[CHB][hapmap];0.82[YRI][hapmap]
rs13186296	0.92[ASN][1000 genomes]
rs171773	0.83[EUR][1000 genomes]
rs2303747	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2546487	0.87[MEX][hapmap]
rs2559990	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256941	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256942	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs256943	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256945	0.80[CEU][hapmap]
rs256947	0.95[ASN][1000 genomes]
rs256948	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs256949	0.94[ASN][1000 genomes]
rs256950	0.95[ASN][1000 genomes]
rs256951	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs256952	0.95[ASN][1000 genomes]
rs256953	0.95[ASN][1000 genomes]
rs256954	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs256955	0.87[CHB][hapmap]
rs256959	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs256962	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]
rs256964	0.80[AMR][1000 genomes]
rs256968	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256976	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs256994	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256996	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377290	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3822579	0.92[ASN][1000 genomes]
rs387718	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs400570	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs413059	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs416234	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs424434	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs428191	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62371215	0.82[ASN][1000 genomes]
rs698365	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[YRI][hapmap]
rs698366	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs698367	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs712550	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712551	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702283	0.95[ASN][1000 genomes]
rs7702869	0.94[ASN][1000 genomes]
rs7702881	0.94[ASN][1000 genomes]
rs790824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790825	0.90[AMR][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
rs9326969	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114938200-114958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:114938200-114960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:114938600-114958000	Weak transcription	Ovary	ovary
4	chr5:114938600-114960000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:114938800-114958600	Weak transcription	Right Ventricle	heart
6	chr5:114938800-114960000	Weak transcription	Lung	lung
7	chr5:114939000-114958000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:114939000-114958000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:114939000-114958200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:114939000-114958800	Weak transcription	Fetal Stomach	stomach
11	chr5:114939000-114959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:114939000-114960200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:114939200-114958800	Weak transcription	Spleen	Spleen
14	chr5:114941000-114959400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:114941400-114958000	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:114945400-114958600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:114945800-114958200	Strong transcription	Primary B cells from cord blood	blood
18	chr5:114946000-114958200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:114946000-114959400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:114946200-114957600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:114946200-114958000	Strong transcription	Dnd41	blood
22	chr5:114946200-114958200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:114946200-114959400	Strong transcription	Fetal Thymus	thymus
24	chr5:114947600-114957800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:114947800-114957600	Strong transcription	HSMM	muscle
26	chr5:114948200-114958000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:114948400-114958200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:114949800-114958000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:114949800-114958200	Strong transcription	HMEC	breast
30	chr5:114950200-114958000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:114951800-114958000	Strong transcription	NHEK	skin
32	chr5:114952400-114958000	Weak transcription	Thymus	Thymus
33	chr5:114952400-114959200	Weak transcription	Brain Germinal Matrix	brain
34	chr5:114952400-114959400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:114952400-114960200	Weak transcription	Esophagus	oesophagus
36	chr5:114952600-114958600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:114953400-114958400	Weak transcription	Stomach Mucosa	stomach
38	chr5:114953800-114958000	Strong transcription	Hela-S3	cervix
39	chr5:114954000-114958200	Strong transcription	NHLF	lung
40	chr5:114954400-114957800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:114954400-114958200	Weak transcription	Left Ventricle	heart
42	chr5:114954400-114960200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:114955000-114958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:114955400-114958000	Weak transcription	Fetal Lung	lung
45	chr5:114955400-114959400	Weak transcription	Fetal Kidney	kidney
46	chr5:114955600-114958000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:114955800-114958000	Weak transcription	Fetal Heart	heart
48	chr5:114955800-114958200	Weak transcription	Brain Substantia Nigra	brain
49	chr5:114955800-114958800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:114955800-114958800	Weak transcription	Psoas Muscle	Psoas

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