Variant report

Variant	rs61924370
Chromosome Location	chr12:42867886-42867887
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	chr12:42867148..42869187-chr12:42983143..42985743,2	K562	blood:
2	chr12:42858838..42861541-chr12:42866075..42868198,2	K562	blood:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10400520	0.86[EUR][1000 genomes]
rs10880289	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880290	0.82[EUR][1000 genomes]
rs10880291	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880292	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880293	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880296	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880299	0.86[EUR][1000 genomes]
rs10880300	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880301	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181430	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181431	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181434	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181436	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181437	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181438	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181440	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181441	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181444	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11181445	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181447	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181448	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181449	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181451	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181457	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181458	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181459	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181460	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181470	0.86[EUR][1000 genomes]
rs11181474	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11181478	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181480	0.86[EUR][1000 genomes]
rs11181481	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11181482	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11181489	0.86[EUR][1000 genomes]
rs11181495	0.86[EUR][1000 genomes]
rs11181498	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11181505	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181506	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11831729	0.86[EUR][1000 genomes]
rs11832055	0.86[EUR][1000 genomes]
rs11834697	0.86[EUR][1000 genomes]
rs11835257	0.86[EUR][1000 genomes]
rs11835826	0.86[EUR][1000 genomes]
rs12227380	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12227738	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12228701	0.86[EUR][1000 genomes]
rs12228962	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12229262	0.87[EUR][1000 genomes]
rs12229735	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12230215	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12230915	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12579754	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12580906	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12581574	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12581958	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1452104	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17091102	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17091176	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2053943	0.89[EUR][1000 genomes]
rs2053945	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2305422	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2406873	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2406874	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2406970	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406971	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897568	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34852216	0.87[EUR][1000 genomes]
rs3810788	0.82[AMR][1000 genomes]
rs3810790	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3810791	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3810792	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3827523	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3852595	0.86[EUR][1000 genomes]
rs3950231	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55645737	0.87[EUR][1000 genomes]
rs55653923	0.86[EUR][1000 genomes]
rs55949213	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56347355	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56404257	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56755189	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58220548	0.80[EUR][1000 genomes]
rs58826545	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58984176	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59844371	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60131710	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60184016	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60846704	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60949933	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61375966	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61471584	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61924349	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61924352	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61924354	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61924355	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61924360	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61924365	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61924368	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61926561	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926562	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926563	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926566	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926568	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926570	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926571	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926572	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926573	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926575	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926588	0.86[EUR][1000 genomes]
rs61926595	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926596	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926597	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926599	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926600	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67215543	0.86[EUR][1000 genomes]
rs73118491	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73118495	0.82[AMR][1000 genomes]
rs73122434	0.87[EUR][1000 genomes]
rs73124421	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs746893	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7955547	0.86[EUR][1000 genomes]
rs7955802	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7956425	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7956485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7958601	0.86[EUR][1000 genomes]
rs7958963	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7959691	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7963726	0.85[EUR][1000 genomes]
rs7966669	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967131	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7970870	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7975971	0.86[EUR][1000 genomes]
rs7976731	0.86[EUR][1000 genomes]
rs974218	0.86[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61924370	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 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	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
4	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
6	chr12:42860200-42868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:42860200-42870400	Weak transcription	Pancreas	Pancrea
8	chr12:42860200-42876200	Weak transcription	Gastric	stomach
9	chr12:42861400-42876000	Weak transcription	Lung	lung
10	chr12:42862800-42876000	Weak transcription	Aorta	Aorta
11	chr12:42863200-42868400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:42863200-42868800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:42863400-42868800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:42863400-42869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:42863400-42869600	Enhancers	Fetal Heart	heart
16	chr12:42863400-42874200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:42863400-42875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:42863400-42876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:42864000-42868800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:42864000-42869000	Weak transcription	Small Intestine	intestine
21	chr12:42864200-42868200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:42864200-42868800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:42864400-42876000	Weak transcription	Spleen	Spleen
24	chr12:42864800-42868800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:42864800-42875600	Weak transcription	Fetal Stomach	stomach
26	chr12:42865000-42869000	Weak transcription	Adipose Nuclei	Adipose
27	chr12:42865000-42869200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:42865200-42868000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:42865200-42868800	Enhancers	Primary B cells from cord blood	blood
30	chr12:42865600-42869200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr12:42866200-42868200	Weak transcription	GM12878-XiMat	blood
32	chr12:42866200-42868600	Enhancers	HMEC	breast
33	chr12:42866200-42869200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:42866200-42869200	Enhancers	NHDF-Ad	bronchial
35	chr12:42866200-42869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:42866200-42876000	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:42866400-42868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:42866400-42869400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr12:42866600-42869000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:42866600-42869200	Enhancers	HSMMtube	muscle
41	chr12:42866600-42869400	Enhancers	Osteobl	bone
42	chr12:42866600-42869600	Enhancers	NHEK	skin
43	chr12:42866600-42870800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:42866800-42868000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:42866800-42868800	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:42866800-42869600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:42867000-42868200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:42867000-42868800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:42867000-42868800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:42867000-42875800	Weak transcription	Right Atrium	heart

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