Variant report

Variant	rs61942484
Chromosome Location	chr12:42504435-42504436
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	chr12:42497518..42500204-chr12:42502639..42504620,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10880252	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181317	0.86[AMR][1000 genomes]
rs11181322	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181344	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532220	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17090898	0.82[AMR][1000 genomes]
rs17494245	0.82[AMR][1000 genomes]
rs3852594	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60631072	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61942482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972986	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61942484	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
2	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
4	chr12:42476000-42524400	Weak transcription	Gastric	stomach
5	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
6	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
7	chr12:42478000-42505000	Weak transcription	Lung	lung
8	chr12:42478600-42511600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:42479600-42505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:42480200-42505600	Weak transcription	Fetal Lung	lung
11	chr12:42480200-42512000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:42480600-42504600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:42483600-42511400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:42484400-42524800	Weak transcription	Right Ventricle	heart
15	chr12:42485200-42511600	Weak transcription	NHDF-Ad	bronchial
16	chr12:42485800-42512200	Weak transcription	Brain Angular Gyrus	brain
17	chr12:42486000-42513000	Weak transcription	Aorta	Aorta
18	chr12:42488200-42505400	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:42488400-42504800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:42488400-42504800	Weak transcription	Fetal Intestine Small	intestine
21	chr12:42488400-42505000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:42488400-42512000	Weak transcription	Osteobl	bone
23	chr12:42488600-42505000	Weak transcription	Fetal Stomach	stomach
24	chr12:42488600-42518600	Weak transcription	Fetal Brain Male	brain
25	chr12:42488800-42511800	Weak transcription	HepG2	liver
26	chr12:42490800-42506600	Weak transcription	NH-A	brain
27	chr12:42490800-42511200	Weak transcription	HSMM	muscle
28	chr12:42491400-42504800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:42491400-42511200	Weak transcription	A549	lung
30	chr12:42492200-42505000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:42492200-42505000	Weak transcription	Ovary	ovary
32	chr12:42492200-42505400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:42492200-42511400	Weak transcription	Adipose Nuclei	Adipose
34	chr12:42492200-42511600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:42492200-42512400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:42492200-42518600	Weak transcription	K562	blood
37	chr12:42492400-42505400	Weak transcription	GM12878-XiMat	blood
38	chr12:42492400-42511400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:42492400-42511600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:42492400-42511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:42492400-42512200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:42492400-42512200	Weak transcription	HUVEC	blood vessel
43	chr12:42492600-42511400	Weak transcription	Dnd41	blood
44	chr12:42492600-42511800	Weak transcription	Primary T cells from cord blood	blood
45	chr12:42493000-42505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:42493000-42511600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:42493000-42511600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:42493000-42524400	Weak transcription	Brain Substantia Nigra	brain
49	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:42493200-42511400	Weak transcription	HMEC	breast

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