Variant report

Variant	rs9436127
Chromosome Location	chr1:150490565-150490566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150254103..150255766-chr1:150487973..150490880,2	MCF-7	breast:
2	chr1:150458274..150463765-chr1:150483214..150490747,8	K562	blood:
3	chr1:150488672..150491336-chr1:150533266..150536212,3	K562	blood:
4	chr1:150458065..150461622-chr1:150486691..150490573,5	MCF-7	breast:
5	chr1:150489113..150492818-chr1:150530627..150535563,5	K562	blood:
6	chr1:150488378..150490694-chr1:150500940..150503568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143374	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000159208	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11205373	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11205385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577600	0.95[CEU][hapmap];0.84[AMR][1000 genomes]
rs11577843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs11581351	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs11582423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11587116	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11587575	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs11590324	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11590787	0.80[AMR][1000 genomes]
rs12023378	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12028001	0.82[AMR][1000 genomes]
rs12029359	0.93[CHB][hapmap];1.00[YRI][hapmap]
rs12040949	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs12042229	0.89[AMR][1000 genomes]
rs12042579	0.90[AMR][1000 genomes]
rs12045304	0.83[AMR][1000 genomes]
rs12046446	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12046899	0.93[CHB][hapmap]
rs1260367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1260389	0.86[AMR][1000 genomes]
rs1260407	0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs1260411	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs1260421	0.85[AMR][1000 genomes]
rs1260459	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498308	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1625468	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1627235	0.85[AMR][1000 genomes]
rs1631973	0.84[AMR][1000 genomes]
rs1694362	0.85[AMR][1000 genomes]
rs1694364	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1694369	0.80[AMR][1000 genomes]
rs1694377	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs1694380	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1694385	0.80[AMR][1000 genomes]
rs17596326	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs17597088	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1815544	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1932934	0.93[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs1972031	0.89[AMR][1000 genomes]
rs2794679	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2794681	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2794684	0.81[AMR][1000 genomes]
rs2794685	0.80[AMR][1000 genomes]
rs2867893	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2867894	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2873669	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs3737240	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820544	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3896342	0.89[AMR][1000 genomes]
rs4446975	0.93[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs4451552	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs45595332	0.84[AMR][1000 genomes]
rs4926395	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4926436	0.82[AMR][1000 genomes]
rs4926437	0.89[AMR][1000 genomes]
rs4971010	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs55742549	0.83[AMR][1000 genomes]
rs55823828	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55928222	0.89[AMR][1000 genomes]
rs55996928	0.86[AMR][1000 genomes]
rs59898460	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes]
rs6672808	0.89[AMR][1000 genomes]
rs6703652	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs696616	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs696618	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs698913	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs698916	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes]
rs698919	0.80[AMR][1000 genomes]
rs698923	0.87[AMR][1000 genomes]
rs7002	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs72696885	0.84[AMR][1000 genomes]
rs72696900	0.82[AMR][1000 genomes]
rs7513205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7523428	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes]
rs7539458	0.89[AMR][1000 genomes]
rs7548085	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7553867	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs828783	0.84[AMR][1000 genomes]
rs832622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs834229	0.87[AMR][1000 genomes]
rs834230	0.87[AMR][1000 genomes]
rs834231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes]
rs834232	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs834234	0.93[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs834242	0.93[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs844309	0.85[AMR][1000 genomes]
rs9436007	0.89[AMR][1000 genomes]
rs9436008	0.86[AMR][1000 genomes]
rs9436112	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs9436115	0.86[AMR][1000 genomes]
rs9436119	0.84[AMR][1000 genomes]
rs9436125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9436127	SNX27	cis	parietal	SCAN
rs9436127	POLR3GL	cis	cerebellum	SCAN
rs9436127	C1orf54	cis	parietal	SCAN
rs9436127	MRPS21	cis	parietal	SCAN
rs9436127	MRPS21	cis	cerebellum	SCAN
rs9436127	MRPS21	Cis_1M	lymphoblastoid	RTeQTL
rs9436127	POGZ	cis	cerebellum	SCAN
rs9436127	TARS2	cis	cerebellum	SCAN
rs9436127	LCE2A	cis	parietal	SCAN
rs9436127	CTSS	cis	cerebellum	SCAN
rs9436127	SEC22B	cis	parietal	SCAN
rs9436127	CTSK	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150489000-150490800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:150489000-150494800	Weak transcription	Esophagus	oesophagus
3	chr1:150489000-150505400	Weak transcription	Right Ventricle	heart
4	chr1:150489200-150490600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr1:150489200-150494400	Weak transcription	Psoas Muscle	Psoas
6	chr1:150489200-150498200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:150489200-150501800	Weak transcription	Right Atrium	heart
8	chr1:150489400-150497000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:150489400-150500200	Weak transcription	Osteobl	bone
10	chr1:150489400-150500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:150489600-150490600	Enhancers	K562	blood
12	chr1:150489600-150498400	Weak transcription	Fetal Stomach	stomach
13	chr1:150489600-150501600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:150490000-150490600	Enhancers	Stomach Mucosa	stomach
15	chr1:150490200-150494200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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