Variant report

Variant	rs256942
Chromosome Location	chr5:114967205-114967206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114965121..114972183-chr5:115175398..115178697,8	MCF-7	breast:
2	chr5:114960793..114963745-chr5:114966203..114968929,3	MCF-7	breast:
3	chr5:114965841..114967612-chr5:114967627..114970927,3	K562	blood:
4	chr5:114949317..114953007-chr5:114964090..114967220,3	K562	blood:

Variant related genes	Relation type
ENSG00000243414	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000145782	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000251201	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10055677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13164545	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13186296	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171774	0.96[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2303747	0.92[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs256941	1.00[ASN][1000 genomes]
rs256944	0.84[CEU][hapmap];0.96[EUR][1000 genomes]
rs256945	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs256947	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256949	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256950	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256951	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256952	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256953	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256954	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256955	0.87[CHB][hapmap]
rs256962	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs256964	0.96[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs256967	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256969	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256988	0.95[EUR][1000 genomes]
rs256991	0.95[EUR][1000 genomes]
rs256993	0.95[EUR][1000 genomes]
rs256997	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256998	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377290	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822579	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs400570	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]
rs413059	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs415577	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs416234	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs424434	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs428191	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4920967	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62371215	0.83[ASN][1000 genomes]
rs698365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs698366	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712550	0.97[ASN][1000 genomes]
rs712551	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7702283	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7702869	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702881	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs790824	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs790825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326969	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]

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
rs256942	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114962400-114971800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:114962600-114967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:114962600-114967400	Weak transcription	Fetal Lung	lung
4	chr5:114962600-114967600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:114962600-114967600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:114962600-114968400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:114962600-114968400	Weak transcription	Liver	Liver
8	chr5:114962600-114968600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:114962600-114968600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:114962600-114969000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:114962600-114969600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:114962600-114969800	Weak transcription	HUVEC	blood vessel
13	chr5:114962600-114969800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:114962600-114970000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:114962800-114970000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:114963000-114969800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:114963000-114969800	Weak transcription	NHDF-Ad	bronchial
18	chr5:114963000-114970000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:114963000-114970000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:114963200-114969800	Weak transcription	Primary T cells from cord blood	blood
21	chr5:114963200-114970000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:114963200-114970000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:114963400-114969000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:114963400-114969800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:114963400-114970000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:114963400-114970000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:114965400-114969200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:114966200-114970000	Weak transcription	K562	blood
29	chr5:114967200-114969000	Weak transcription	HepG2	liver

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