Variant report

Variant	rs824741
Chromosome Location	chr12:42559236-42559237
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42538565..42540074-chr12:42559024..42561176,2	K562	blood:
2	chr12:42537581..42540065-chr12:42557796..42560524,2	K562	blood:
3	chr12:42559136..42560641-chr12:42595812..42598581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151233	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1069644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785335	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785337	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10880275	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880279	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10880280	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10880284	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs11181461	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1118483	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1226298	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1226303	0.93[JPT][hapmap]
rs1238290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423383	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs12578312	0.81[CEU][hapmap]
rs1463613	0.93[JPT][hapmap]
rs1628871	0.92[JPT][hapmap]
rs1683195	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17091052	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1732351	0.87[JPT][hapmap]
rs1732352	0.87[JPT][hapmap]
rs1826387	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2061191	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2061192	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2100547	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198763	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2605401	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3761677	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs3827524	0.90[CHB][hapmap]
rs4402364	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417370	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768397	0.91[CHB][hapmap]
rs4768398	0.85[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs4768401	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs6582378	0.87[JPT][hapmap]
rs6582385	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582386	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6582389	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6582392	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712106	0.93[JPT][hapmap]
rs712108	0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712109	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712112	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712114	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712115	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712118	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs712120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs712122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712126	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs712127	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs712129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712130	0.82[EUR][1000 genomes]
rs7298965	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7302687	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316575	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7956016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7959339	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960176	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975518	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7978993	0.87[JPT][hapmap]
rs824716	0.87[JPT][hapmap]
rs824724	0.87[JPT][hapmap]
rs824734	0.93[JPT][hapmap]
rs824738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs824739	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs824742	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs844046	0.93[JPT][hapmap]
rs865420	0.93[JPT][hapmap]
rs866091	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs824741	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
3	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
6	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
9	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
10	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
11	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:42546000-42564400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:42547200-42563800	Weak transcription	Fetal Stomach	stomach
14	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:42549400-42575000	Weak transcription	Brain Angular Gyrus	brain
16	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:42550800-42568400	Weak transcription	Right Ventricle	heart
18	chr12:42552000-42604000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:42552200-42574800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:42552200-42591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:42552200-42613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
23	chr12:42552600-42578800	Weak transcription	Lung	lung
24	chr12:42552800-42564400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:42553400-42571200	Weak transcription	Esophagus	oesophagus
26	chr12:42553600-42590000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:42554000-42562800	Weak transcription	Small Intestine	intestine
28	chr12:42554000-42607600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:42554400-42564200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:42554400-42578600	Weak transcription	Thymus	Thymus
31	chr12:42554600-42561600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:42554600-42563400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:42554600-42568200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:42554600-42570800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:42554600-42592200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:42554800-42568800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:42554800-42571000	Weak transcription	HepG2	liver
38	chr12:42555000-42564200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:42555000-42565200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:42555000-42565600	Weak transcription	Fetal Thymus	thymus
41	chr12:42555000-42566600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:42555000-42568800	Weak transcription	HSMM	muscle
43	chr12:42555000-42628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:42555200-42564400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:42555200-42566600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:42555200-42567000	Weak transcription	Adipose Nuclei	Adipose
47	chr12:42555200-42570200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:42555200-42572600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:42555200-42574800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:42555200-42575400	Weak transcription	NH-A	brain

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