Variant report

Variant	rs7964383
Chromosome Location	chr12:42482978-42482979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42477798..42480028-chr12:42482266..42483853,2	K562	blood:
2	chr12:42473066..42475220-chr12:42482605..42484147,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222884	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1064469	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes]
rs10785325	0.82[AMR][1000 genomes]
rs10785326	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10785327	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785330	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880223	0.80[AMR][1000 genomes]
rs10880229	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10880231	0.85[AMR][1000 genomes]
rs10880238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880239	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880242	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880253	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880254	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11181315	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11181330	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181333	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1226303	0.84[MEX][hapmap]
rs1238290	0.83[MEX][hapmap]
rs1683195	0.83[MEX][hapmap]
rs3990966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582378	0.84[MEX][hapmap]
rs6582381	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582382	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582384	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67706143	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs712119	0.83[MEX][hapmap]
rs712123	0.83[MEX][hapmap]
rs7133752	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135595	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136450	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137522	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7296707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297971	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7298106	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7303028	0.88[MEX][hapmap]
rs7305104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7315891	0.82[AMR][1000 genomes]
rs7956016	0.83[MEX][hapmap]
rs7959417	0.82[AMR][1000 genomes]
rs7959852	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971943	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7975518	0.83[MEX][hapmap]
rs824734	0.88[MEX][hapmap]
rs865420	0.83[MEX][hapmap]
rs9738145	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9739472	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	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
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2025559	chr12:42481619-42491335	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7964383	PPHLN1	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42464600-42484000	Weak transcription	HSMM	muscle
2	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
3	chr12:42469400-42491800	Weak transcription	Ovary	ovary
4	chr12:42470400-42484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:42470600-42484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:42470800-42485600	Weak transcription	Aorta	Aorta
8	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:42471200-42483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:42471400-42485600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:42471800-42483400	Weak transcription	Fetal Stomach	stomach
12	chr12:42471800-42486600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
14	chr12:42472200-42487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:42472800-42489000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:42473600-42483600	Weak transcription	Adipose Nuclei	Adipose
17	chr12:42473600-42484000	Weak transcription	HUVEC	blood vessel
18	chr12:42473600-42484200	Weak transcription	Primary T cells from cord blood	blood
19	chr12:42473800-42484000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:42474000-42484000	Weak transcription	NH-A	brain
21	chr12:42474000-42484200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:42474000-42496000	Weak transcription	Fetal Intestine Large	intestine
23	chr12:42474200-42484000	Weak transcription	Osteobl	bone
24	chr12:42474200-42486000	Weak transcription	GM12878-XiMat	blood
25	chr12:42474200-42487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:42474200-42490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
29	chr12:42474800-42487600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:42474800-42487600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:42474800-42491800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:42475000-42484200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:42475000-42491800	Weak transcription	Brain Substantia Nigra	brain
34	chr12:42475400-42485600	Weak transcription	Left Ventricle	heart
35	chr12:42476000-42485600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:42476000-42524400	Weak transcription	Gastric	stomach
37	chr12:42476200-42487000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
39	chr12:42476400-42487400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:42476400-42487600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:42476400-42489800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
43	chr12:42476800-42483400	Weak transcription	Fetal Kidney	kidney
44	chr12:42476800-42484200	Weak transcription	NHEK	skin
45	chr12:42477000-42484000	Weak transcription	NHDF-Ad	bronchial
46	chr12:42477600-42490400	Weak transcription	Thymus	Thymus
47	chr12:42478000-42484200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:42478000-42489000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:42478000-42505000	Weak transcription	Lung	lung
50	chr12:42478200-42483400	Weak transcription	Placenta	Placenta

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