Variant report

Variant	rs12430152
Chromosome Location	chr13:96472037-96472038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96471414..96473149-chr13:96476270..96478786,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10508027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11616953	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11618323	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12583796	0.93[YRI][hapmap]
rs16951334	0.85[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs17878753	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17879875	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1788062	1.00[JPT][hapmap]
rs17885081	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1854758	1.00[JPT][hapmap]
rs3087341	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099362	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3099363	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3101570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3125439	0.87[AMR][1000 genomes]
rs3848077	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886352	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3901894	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs4254181	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4347496	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4383020	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4409947	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4491364	0.95[ASN][1000 genomes]
rs4526890	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs565898	1.00[JPT][hapmap]
rs6492821	0.93[YRI][hapmap]
rs6492822	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72636541	0.87[EUR][1000 genomes]
rs7316996	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7318892	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7323408	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]
rs7331211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331549	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332078	1.00[JPT][hapmap]
rs7334320	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7334552	0.93[YRI][hapmap]
rs7339059	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7991405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7999737	1.00[JPT][hapmap]
rs816142	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs9302084	0.92[YRI][hapmap]
rs9516621	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9525079	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9561931	0.82[YRI][hapmap]
rs9561939	0.89[YRI][hapmap]
rs9584324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590310	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9590328	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[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	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3509289	chr13:96461000-96505090	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3509290	chr13:96461000-96505090	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12430152	DZIP1	cis	parietal	SCAN
rs12430152	DZIP1	Cis_1M	lymphoblastoid	RTeQTL
rs12430152	UGCGL2	cis	multi-tissue	Pritchard
rs12430152	UGGT2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96444400-96477600	Weak transcription	Brain Angular Gyrus	brain
2	chr13:96444400-96477600	Weak transcription	NHLF	lung
3	chr13:96444400-96485600	Weak transcription	NHDF-Ad	bronchial
4	chr13:96445600-96477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:96445800-96490000	Weak transcription	HepG2	liver
6	chr13:96446200-96477400	Weak transcription	Gastric	stomach
7	chr13:96446800-96477400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:96446800-96477400	Weak transcription	HSMMtube	muscle
9	chr13:96447200-96477400	Weak transcription	Osteobl	bone
10	chr13:96452000-96490600	Weak transcription	Fetal Kidney	kidney
11	chr13:96458800-96477400	Weak transcription	NH-A	brain
12	chr13:96460400-96477200	Weak transcription	A549	lung
13	chr13:96460400-96477400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:96462000-96477400	Weak transcription	HSMM	muscle
15	chr13:96462200-96477200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:96462200-96477400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:96462600-96485600	Weak transcription	Hela-S3	cervix
18	chr13:96465600-96481200	Weak transcription	Psoas Muscle	Psoas
19	chr13:96466200-96476600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:96466200-96477400	Weak transcription	Fetal Intestine Large	intestine
21	chr13:96466200-96477800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr13:96466200-96480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:96466200-96481400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:96466400-96477200	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:96466400-96477400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:96466400-96485400	Weak transcription	NHEK	skin
27	chr13:96466400-96486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:96466600-96476600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:96466600-96477200	Weak transcription	Brain Germinal Matrix	brain
30	chr13:96466600-96477200	Weak transcription	Fetal Lung	lung
31	chr13:96466600-96477400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr13:96466600-96477400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:96466600-96477400	Weak transcription	Liver	Liver
34	chr13:96466600-96477400	Weak transcription	Left Ventricle	heart
35	chr13:96466600-96477400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:96466600-96477400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr13:96466600-96477600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:96466600-96477800	Weak transcription	Spleen	Spleen
39	chr13:96466600-96485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:96466800-96477200	Weak transcription	Fetal Brain Female	brain
41	chr13:96466800-96477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:96466800-96477400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr13:96466800-96477400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:96466800-96477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr13:96466800-96477400	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:96466800-96477400	Weak transcription	Fetal Stomach	stomach
47	chr13:96466800-96477600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr13:96466800-96485800	Weak transcription	Brain Anterior Caudate	brain
49	chr13:96467000-96474000	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:96467000-96476800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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