Variant report

Variant	rs12513108
Chromosome Location	chr4:110754499-110754500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10020617	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022841	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516559	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs11937249	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12500239	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12504835	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12508007	0.83[MKK][hapmap]
rs12510851	0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12643147	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12644142	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13107617	1.00[CHB][hapmap]
rs13109228	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112387	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13115969	0.94[CEU][hapmap]
rs13128244	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs13128301	1.00[CHB][hapmap]
rs13129185	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140289	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13141065	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150454	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2078040	0.94[CEU][hapmap]
rs2347130	0.94[CEU][hapmap];0.85[TSI][hapmap]
rs2347131	0.86[ASW][hapmap];0.88[CEU][hapmap];0.85[TSI][hapmap]
rs2347132	0.86[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[TSI][hapmap]
rs2347133	0.88[CEU][hapmap]
rs34378309	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34706258	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34717063	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34734592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35426158	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36101562	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775961	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353905	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4422417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610335	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698750	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698795	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs6814743	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6816185	0.94[CEU][hapmap]
rs6841737	0.94[CEU][hapmap]
rs6842245	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858351	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7442158	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7657133	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678178	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7684459	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698794	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9993509	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12513108	LRIT3	cis	cerebellum	SCAN
rs12513108	ENPEP	cis	cerebellum	SCAN
rs12513108	GAR1	cis	cerebellum	SCAN
rs12513108	GAR1	cis	parietal	SCAN
rs12513108	RRH	cis	parietal	SCAN
rs12513108	CYP2U1	cis	parietal	SCAN
rs12513108	RRH	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
2	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:110742200-110764400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:110744000-110759600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:110744400-110774400	Weak transcription	Psoas Muscle	Psoas
7	chr4:110744600-110773200	Weak transcription	Primary T cells from cord blood	blood
8	chr4:110746400-110764000	Weak transcription	Primary B cells from cord blood	blood
9	chr4:110746600-110761200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:110746800-110759400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:110746800-110767600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:110747000-110754800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:110747000-110757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:110747200-110756400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:110747600-110758400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:110749600-110757600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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