Variant report

Variant	rs400570
Chromosome Location	chr5:114951553-114951554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114950483..114953448-chr5:115177527..115180006,2	K562	blood:
2	chr5:114938188..114939969-chr5:114950245..114952117,2	K562	blood:
3	chr5:114950362..114952033-chr5:115173544..115175106,2	K562	blood:
4	chr5:114949905..114952217-chr5:114956239..114958053,2	K562	blood:

Variant related genes	Relation type
ENSG00000249249	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000145782	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10055677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13164545	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13186296	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs171774	0.96[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2303747	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs256941	0.97[ASN][1000 genomes]
rs256942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256944	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256945	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256947	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256948	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256949	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256950	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256951	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256952	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256953	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256954	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256955	0.87[CHB][hapmap]
rs256962	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs256964	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs256967	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256969	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256988	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256991	0.94[EUR][1000 genomes]
rs256993	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256996	0.81[AMR][1000 genomes]
rs256997	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs256998	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs377290	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822579	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs413059	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs415577	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs416234	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs424434	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4920967	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62371215	0.82[ASN][1000 genomes]
rs698365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs698366	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs698367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712550	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs712551	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7702283	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7702869	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7702881	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs790824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs790825	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326969	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]

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
rs400570	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr5:114938200-114957200	Weak transcription	Small Intestine	intestine
3	chr5:114938200-114958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:114938200-114960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:114938600-114951600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:114938600-114951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:114938600-114951800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:114938600-114951800	Weak transcription	Esophagus	oesophagus
9	chr5:114938600-114958000	Weak transcription	Ovary	ovary
10	chr5:114938600-114960000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:114938800-114951600	Weak transcription	K562	blood
12	chr5:114938800-114951800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:114938800-114951800	Weak transcription	Thymus	Thymus
14	chr5:114938800-114951800	Weak transcription	NHLF	lung
15	chr5:114938800-114952000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:114938800-114953800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:114938800-114954000	Weak transcription	Fetal Brain Female	brain
18	chr5:114938800-114954200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:114938800-114954200	Weak transcription	Colonic Mucosa	Colon
20	chr5:114938800-114957400	Weak transcription	Aorta	Aorta
21	chr5:114938800-114958600	Weak transcription	Right Ventricle	heart
22	chr5:114938800-114960000	Weak transcription	Lung	lung
23	chr5:114939000-114955200	Weak transcription	Fetal Heart	heart
24	chr5:114939000-114957200	Weak transcription	Fetal Brain Male	brain
25	chr5:114939000-114957200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:114939000-114957200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:114939000-114957400	Weak transcription	Pancreas	Pancrea
28	chr5:114939000-114958000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:114939000-114958000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:114939000-114958200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:114939000-114958800	Weak transcription	Fetal Stomach	stomach
32	chr5:114939000-114959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:114939000-114960200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:114939200-114951800	Weak transcription	NHEK	skin
35	chr5:114939200-114952600	Weak transcription	Stomach Mucosa	stomach
36	chr5:114939200-114954000	Weak transcription	Brain Anterior Caudate	brain
37	chr5:114939200-114954200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:114939200-114954600	Weak transcription	Brain Substantia Nigra	brain
39	chr5:114939200-114957200	Weak transcription	Brain Angular Gyrus	brain
40	chr5:114939200-114958800	Weak transcription	Spleen	Spleen
41	chr5:114940400-114957200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:114941000-114959400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:114941400-114958000	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:114944000-114954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:114944000-114954800	Weak transcription	Psoas Muscle	Psoas
46	chr5:114944200-114953800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:114944200-114957200	Weak transcription	Gastric	stomach
48	chr5:114944600-114954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:114944600-114954200	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:114945400-114958600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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