Variant report

Variant	rs2347131
Chromosome Location	chr4:110791361-110791362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10022841	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs11098049	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12498239	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500239	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12504835	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs12508179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513108	0.86[ASW][hapmap];0.88[CEU][hapmap];0.85[TSI][hapmap]
rs12643147	0.86[ASN][1000 genomes]
rs12644142	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs13112387	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13115969	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125596	0.88[EUR][1000 genomes]
rs13140289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13141065	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs13150454	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs17040920	0.82[MKK][hapmap]
rs1860130	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2078040	0.94[CEU][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347130	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347132	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34378309	0.86[ASN][1000 genomes]
rs34706258	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34717063	0.81[AMR][1000 genomes]
rs35043368	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35426158	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3775961	0.83[CEU][hapmap]
rs4353905	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs4422417	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs4610335	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs4698749	0.88[CEU][hapmap]
rs4698750	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4698751	0.84[EUR][1000 genomes]
rs4698799	0.89[EUR][1000 genomes]
rs55814498	0.81[EUR][1000 genomes]
rs6814655	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814743	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6816185	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842245	0.81[CEU][hapmap]
rs6858351	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7657133	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7678178	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7698794	0.84[AMR][1000 genomes];0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2347131	RRH	cis	cerebellum	SCAN
rs2347131	GAR1	cis	cerebellum	SCAN
rs2347131	ENPEP	cis	cerebellum	SCAN
rs2347131	LRIT3	cis	cerebellum	SCAN
rs2347131	CYP2U1	cis	parietal	SCAN
rs2347131	RRH	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110780400-110795000	Weak transcription	Esophagus	oesophagus
2	chr4:110786200-110796600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:110789600-110794800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:110789600-110795800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:110789800-110792400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:110789800-110793600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:110789800-110798400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:110790000-110792600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:110790400-110792800	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:110790600-110791400	Strong transcription	Pancreas	Pancrea
11	chr4:110790600-110791600	ZNF genes & repeats	Brain Substantia Nigra	brain
12	chr4:110790600-110791600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr4:110790600-110791800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:110790600-110792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:110790800-110791600	Strong transcription	Adipose Nuclei	Adipose
16	chr4:110790800-110791600	Strong transcription	Aorta	Aorta
17	chr4:110790800-110791600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:110790800-110791800	Strong transcription	Brain Angular Gyrus	brain
19	chr4:110791000-110791800	Strong transcription	Primary T cells from cord blood	blood
20	chr4:110791200-110791800	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr4:110791200-110791800	Strong transcription	Gastric	stomach
22	chr4:110791200-110791800	ZNF genes & repeats	Lung	lung

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