Variant report

Variant	rs6582398
Chromosome Location	chr12:42870444-42870445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42869596..42873194-chr12:42873699..42877854,4	K562	blood:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1051453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880283	0.82[ASN][1000 genomes]
rs10880294	0.81[EUR][1000 genomes]
rs11181422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11181454	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181463	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181465	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11181466	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181467	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181483	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181499	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181501	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181502	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181507	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12228205	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12815283	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12820154	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1551210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669886	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669892	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669893	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669904	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669907	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1669910	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17551006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796380	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796381	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796384	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796386	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1796388	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796394	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839935	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2178753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406674	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2600908	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708058	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3747558	0.83[ASN][1000 genomes]
rs3747560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3810793	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768399	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768402	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768411	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768413	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55702525	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56051354	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56290913	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926593	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582395	0.82[ASN][1000 genomes]
rs7133836	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7296357	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7305397	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307790	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959338	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965743	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969910	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7970003	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6582398	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs6582398	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs6582398	PPHLN1	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
3	chr12:42860200-42876200	Weak transcription	Gastric	stomach
4	chr12:42861400-42876000	Weak transcription	Lung	lung
5	chr12:42862800-42876000	Weak transcription	Aorta	Aorta
6	chr12:42863400-42874200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:42863400-42875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:42863400-42876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:42864400-42876000	Weak transcription	Spleen	Spleen
10	chr12:42864800-42875600	Weak transcription	Fetal Stomach	stomach
11	chr12:42866200-42876000	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:42866600-42870800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:42867000-42875800	Weak transcription	Right Atrium	heart
14	chr12:42867200-42874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:42867200-42875800	Weak transcription	Ovary	ovary
16	chr12:42867400-42872200	Weak transcription	Fetal Lung	lung
17	chr12:42867400-42873200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:42867400-42874600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:42869000-42871400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:42869000-42873000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:42869200-42870600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:42869200-42872200	Weak transcription	HSMMtube	muscle
23	chr12:42869200-42872800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:42869200-42873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:42869200-42874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:42869200-42874400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:42869200-42875400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:42869200-42875400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:42869400-42871400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:42869400-42871400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:42869400-42871400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:42869400-42871800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:42869400-42872200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:42869400-42872400	Weak transcription	Small Intestine	intestine
35	chr12:42869400-42872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:42869400-42874400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:42869400-42874400	Weak transcription	Osteobl	bone
38	chr12:42869400-42874600	Weak transcription	Left Ventricle	heart
39	chr12:42869400-42875200	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:42869400-42875200	Weak transcription	NHLF	lung
41	chr12:42869400-42875800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:42869400-42875800	Weak transcription	HSMM	muscle
43	chr12:42869400-42876000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:42869400-42876000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:42869400-42876400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:42869600-42871600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:42869600-42871600	Weak transcription	HUVEC	blood vessel
48	chr12:42869600-42871800	Weak transcription	Fetal Heart	heart
49	chr12:42869600-42872400	Weak transcription	Fetal Kidney	kidney
50	chr12:42869600-42872400	Weak transcription	GM12878-XiMat	blood

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