Variant report

Variant	rs12084338
Chromosome Location	chr1:228377913-228377914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228375523..228377154-chr1:228377269..228379542,2	MCF-7	breast:
2	chr1:228371942..228373821-chr1:228377603..228380001,2	K562	blood:
3	chr1:228361597..228363639-chr1:228376679..228379566,3	K562	blood:
4	chr1:228367725..228372821-chr1:228377689..228380181,6	MCF-7	breast:
5	chr1:228350293..228354874-chr1:228377436..228381142,4	MCF-7	breast:
6	chr1:228376793..228379462-chr1:228393288..228395336,2	K562	blood:
7	chr1:228352988..228354988-chr1:228376364..228379322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1059778	0.84[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10753445	0.84[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10799468	0.82[EUR][1000 genomes]
rs10799469	0.85[AFR][1000 genomes]
rs10916268	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs10916271	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10916277	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11584385	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs12097591	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12130630	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134624	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12564763	0.92[TSI][hapmap]
rs12745416	0.84[CEU][hapmap]
rs1411910	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs1411911	0.85[EUR][1000 genomes]
rs1557026	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1620111	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs1629294	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1745423	0.87[YRI][hapmap]
rs1757132	0.84[CEU][hapmap]
rs1757133	0.84[CEU][hapmap]
rs1757139	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1757147	0.84[CEU][hapmap]
rs1757149	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1757150	0.84[CEU][hapmap]
rs1757152	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1757156	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs17623766	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17640616	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1771459	0.84[CEU][hapmap]
rs1771460	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1771461	0.83[CEU][hapmap]
rs1771462	0.83[CEU][hapmap]
rs1771467	0.84[CEU][hapmap]
rs1771472	0.83[CEU][hapmap]
rs1771474	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1771476	0.84[CEU][hapmap]
rs1771479	0.84[CEU][hapmap]
rs1771482	0.84[CEU][hapmap]
rs1771483	0.84[CEU][hapmap]
rs1771484	0.91[CEU][hapmap]
rs1771485	0.84[CEU][hapmap]
rs1771487	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs2066237	0.84[CEU][hapmap];0.95[TSI][hapmap]
rs2185544	0.85[EUR][1000 genomes]
rs2298014	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2313600	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2313601	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs2313602	0.84[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2776855	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2776856	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2872538	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs3121309	0.87[YRI][hapmap]
rs4653536	0.84[EUR][1000 genomes]
rs4653907	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653915	0.80[EUR][1000 genomes]
rs4653917	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653919	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653920	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653921	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55658545	0.86[EUR][1000 genomes]
rs55873533	0.94[EUR][1000 genomes]
rs61825279	0.82[EUR][1000 genomes]
rs6426492	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes]
rs6657968	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6661539	0.86[EUR][1000 genomes]
rs6673893	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6682260	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs708124	0.87[YRI][hapmap]
rs72757811	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72757812	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72757824	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72757827	0.95[EUR][1000 genomes]
rs72757829	0.89[EUR][1000 genomes]
rs7512209	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7515849	0.81[YRI][hapmap]
rs752107	0.82[ASW][hapmap]
rs7523917	0.82[TSI][hapmap]
rs7532141	0.84[EUR][1000 genomes]
rs7532924	0.84[CEU][hapmap]
rs7537636	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7539762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs766972	0.83[ASW][hapmap]
rs822725	0.82[TSI][hapmap]
rs849749	0.87[TSI][hapmap]
rs947087	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs947631	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12084338	MRPL55	cis	parietal	SCAN
rs12084338	ITPKB	cis	cerebellum	SCAN
rs12084338	OBSCN	cis	Esophagus Mucosa	GTEx
rs12084338	WDR26	cis	cerebellum	SCAN
rs12084338	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs12084338	IBA57	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
4	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
6	chr1:228364000-228384800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:228365000-228379600	Weak transcription	Gastric	stomach
12	chr1:228365000-228380400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
14	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:228365800-228382600	Weak transcription	Spleen	Spleen
16	chr1:228366000-228386400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:228366800-228379600	Weak transcription	Placenta	Placenta
18	chr1:228366800-228385200	Weak transcription	Ovary	ovary
19	chr1:228366800-228386600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
21	chr1:228369600-228379600	Weak transcription	Lung	lung
22	chr1:228369800-228379600	Weak transcription	Psoas Muscle	Psoas
23	chr1:228370000-228378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:228371200-228386400	Weak transcription	Primary T cells from cord blood	blood
25	chr1:228372400-228379600	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:228373600-228382600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:228373800-228386200	Weak transcription	Fetal Stomach	stomach
28	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:228376400-228382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:228376400-228385200	Weak transcription	Fetal Brain Female	brain
31	chr1:228377600-228378800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:228377800-228380800	Enhancers	Fetal Muscle Trunk	muscle

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