Variant report

Variant	rs9332467
Chromosome Location	chr4:99795324-99795325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADH5-6	chr4:99792836-99795886	NONHSAT097499

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10007957	0.97[ASN][1000 genomes]
rs10008093	0.97[ASN][1000 genomes]
rs10010610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10011791	0.90[ASN][1000 genomes]
rs10019506	0.94[ASN][1000 genomes]
rs10020687	0.98[ASN][1000 genomes]
rs10022521	0.94[ASN][1000 genomes]
rs10023577	0.88[CEU][hapmap]
rs10032966	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10035037	0.84[CEU][hapmap]
rs10212891	0.89[ASN][1000 genomes]
rs1036946	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10433890	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10433891	1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs10433976	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs10461135	0.97[ASN][1000 genomes]
rs10470955	0.99[ASN][1000 genomes]
rs10516437	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11723037	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs11725932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11728783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729285	0.81[EUR][1000 genomes]
rs11737130	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737186	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1230147	0.89[ASN][1000 genomes]
rs1230149	0.88[ASN][1000 genomes]
rs1230150	0.88[ASN][1000 genomes]
rs1230152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1230189	0.89[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs12498533	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs12644580	0.88[CEU][hapmap]
rs13110531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs17028238	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17028241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17028244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17028293	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17550514	0.97[ASN][1000 genomes]
rs2123782	0.84[CEU][hapmap]
rs2602889	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs28367437	0.94[ASN][1000 genomes]
rs28376834	0.94[ASN][1000 genomes]
rs28430857	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28473608	0.97[ASN][1000 genomes]
rs28499420	0.94[ASN][1000 genomes]
rs28529446	0.94[ASN][1000 genomes]
rs28575093	0.99[ASN][1000 genomes]
rs28577966	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28589528	0.90[ASN][1000 genomes]
rs28613604	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622595	0.90[ASN][1000 genomes]
rs28633499	0.97[ASN][1000 genomes]
rs3133161	0.89[ASN][1000 genomes]
rs35447189	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699686	0.85[AMR][1000 genomes]
rs4699687	0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs4699688	0.81[EUR][1000 genomes]
rs4699693	0.88[CEU][hapmap]
rs60120090	0.97[ASN][1000 genomes]
rs60658326	0.97[ASN][1000 genomes]
rs6532774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6810489	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6811070	0.83[EUR][1000 genomes]
rs6815444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6822589	0.84[CEU][hapmap]
rs6830125	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841295	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846266	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848246	0.84[CEU][hapmap]
rs6852715	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs72677504	0.97[ASN][1000 genomes]
rs72692622	0.99[ASN][1000 genomes]
rs7660937	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661487	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7664964	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666015	0.89[ASN][1000 genomes]
rs7671306	0.99[ASN][1000 genomes]
rs7671453	0.99[ASN][1000 genomes]
rs7674319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676259	0.84[CEU][hapmap]
rs7676504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7679685	0.90[ASN][1000 genomes]
rs7684964	0.94[ASN][1000 genomes]
rs7696573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697071	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9995478	0.89[ASN][1000 genomes]
rs9996959	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9999702	0.90[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9332467	ADH5	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99785400-99798800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:99790800-99805400	Weak transcription	Fetal Lung	lung
3	chr4:99791200-99798800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:99792200-99795400	Enhancers	K562	blood
5	chr4:99792400-99825000	Weak transcription	Gastric	stomach
6	chr4:99792600-99804000	Weak transcription	HUVEC	blood vessel
7	chr4:99792800-99797600	Weak transcription	HSMM	muscle
8	chr4:99792800-99799000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:99793000-99800800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:99793400-99803000	Weak transcription	Stomach Mucosa	stomach
11	chr4:99794200-99797600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:99794400-99798800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:99794400-99802600	Weak transcription	NHLF	lung
14	chr4:99794600-99797400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:99794600-99797600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:99794600-99797600	Weak transcription	NH-A	brain
17	chr4:99794600-99799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:99794600-99800600	Weak transcription	HMEC	breast
19	chr4:99794600-99800600	Weak transcription	NHDF-Ad	bronchial
20	chr4:99794600-99802000	Weak transcription	Osteobl	bone
21	chr4:99794600-99802200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:99794600-99802800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:99794600-99802800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:99794600-99804800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:99794600-99805600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:99794600-99805600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:99794800-99797400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:99794800-99797400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:99794800-99798200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:99794800-99800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:99794800-99802600	Weak transcription	NHEK	skin
32	chr4:99795000-99800600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:99795000-99807000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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