Variant report

Variant	rs9855442
Chromosome Location	chr3:51318275-51318276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10212250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1031925	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs11130274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11130280	0.91[CEU][hapmap]
rs11130282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11130286	0.91[CEU][hapmap]
rs11130290	0.91[CEU][hapmap]
rs11706571	0.91[CEU][hapmap]
rs12494165	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12635282	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1318649	0.91[CEU][hapmap]
rs1383251	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1383252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480355	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480357	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480358	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]
rs1480360	0.91[CEU][hapmap]
rs1480362	0.92[CEU][hapmap]
rs1480363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480364	0.91[CEU][hapmap]
rs1480365	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1542574	0.86[JPT][hapmap]
rs1552072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552074	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs17051762	0.86[JPT][hapmap]
rs1904786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061950	0.92[CEU][hapmap]
rs2061951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2127655	0.86[JPT][hapmap]
rs2170178	0.91[CEU][hapmap]
rs2219891	0.91[CEU][hapmap]
rs2355934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2355941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355942	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355943	0.91[CEU][hapmap]
rs2883809	0.91[CEU][hapmap]
rs2883811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34035394	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34251985	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856932	0.84[CEU][hapmap]
rs4244696	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4244697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4244704	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4267675	0.88[JPT][hapmap]
rs4286453	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4301044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4309763	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4328835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4367100	0.91[CEU][hapmap]
rs4367101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4378999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4446244	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4453876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4475072	0.85[CEU][hapmap]
rs4478114	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4528983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4532165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4538365	0.92[CEU][hapmap]
rs4557148	0.92[CEU][hapmap]
rs4560329	0.91[CEU][hapmap]
rs4568177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4589968	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4927970	0.92[CEU][hapmap]
rs4927978	1.00[YRI][hapmap]
rs4927983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4974092	0.91[CEU][hapmap]
rs4974093	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4974094	0.91[CEU][hapmap]
rs4974095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974099	0.91[CEU][hapmap]
rs4974105	0.84[CHB][hapmap]
rs4974108	0.91[CEU][hapmap]
rs4974109	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6445549	0.91[CEU][hapmap]
rs6445551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6445601	0.91[CEU][hapmap]
rs6445604	0.91[CEU][hapmap]
rs6445611	0.91[CEU][hapmap]
rs6445620	0.84[CHB][hapmap]
rs6445622	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6445628	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6446011	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6446118	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6446167	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6446168	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs67086923	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6772664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6777719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6779658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6782946	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784455	0.91[CEU][hapmap]
rs6787805	0.91[CEU][hapmap]
rs6793613	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6793648	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6796847	0.91[CEU][hapmap]
rs6800805	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6809080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs73834002	0.88[AFR][1000 genomes]
rs7427006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs751075	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7611873	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7615291	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7619584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7625006	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs7628533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7629433	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7630714	0.90[CEU][hapmap]
rs7630730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7634514	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7634799	0.91[CEU][hapmap]
rs7640083	0.91[CEU][hapmap]
rs7640263	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7644957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7649069	0.91[CEU][hapmap]
rs7651141	0.92[CEU][hapmap]
rs7652655	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7652818	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7653451	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs899750	0.91[CEU][hapmap]
rs922612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9683267	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814041	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9825454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827072	1.00[CEU][hapmap]
rs9828200	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9832672	0.91[CEU][hapmap]
rs9844581	0.92[CEU][hapmap]
rs9847479	0.92[CEU][hapmap]
rs9855454	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856566	0.92[CEU][hapmap]
rs9858412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9860403	0.91[CEU][hapmap]
rs9860962	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9869123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9871539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9877188	0.91[CEU][hapmap]
rs9878100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs995543	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv3345273	chr3:51318261-51318627	Strong transcription Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9855442	TEX264	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:51296400-51318800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:51298400-51319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:51305000-51318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:51311200-51319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:51312200-51319000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:51312200-51319200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:51313000-51322800	Weak transcription	HSMMtube	muscle
12	chr3:51313000-51323800	Weak transcription	Fetal Brain Male	brain
13	chr3:51313400-51321800	Weak transcription	Right Ventricle	heart
14	chr3:51313400-51322800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:51315600-51319000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:51316000-51320600	Weak transcription	Fetal Brain Female	brain
18	chr3:51316600-51318600	Enhancers	Brain Substantia Nigra	brain
19	chr3:51317000-51319800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:51317400-51318400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:51317400-51319000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:51317800-51319000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:51317800-51320600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:51317800-51322200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:51318000-51322000	Weak transcription	Brain Anterior Caudate	brain
26	chr3:51318200-51319200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:51318200-51320600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:51318200-51320800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:51318200-51328600	Weak transcription	Brain Inferior Temporal Lobe	brain

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