Variant report

Variant	rs7975632
Chromosome Location	chr12:48443048-48443049
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	chr12:48440309..48443140-chr12:48444434..48446613,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10161358	0.81[EUR][1000 genomes]
rs10875716	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs10875718	0.88[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs10875719	0.88[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes]
rs10875721	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10875749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs11168338	0.83[LWK][hapmap]
rs11168351	0.82[ASW][hapmap];0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11168408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11168411	1.00[LWK][hapmap]
rs11168428	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168437	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12228750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368659	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12816820	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1476607	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408955	0.86[GIH][hapmap]
rs3997	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4760679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6580652	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs7486941	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap]
rs7487682	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap]
rs7971880	0.88[CEU][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs8716	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs9971924	0.86[EUR][1000 genomes];1.00[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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7975632	RPAP3	cis	cerebellum	SCAN
rs7975632	SENP1	cis	parietal	SCAN
rs7975632	PFKM	cis	parietal	SCAN
rs7975632	DDX23	cis	parietal	SCAN
rs7975632	H1FNT	cis	Muscle Skeletal	GTEx
rs7975632	RP1-228P16.1	cis	Artery Tibial	GTEx
rs7975632	C12orf68	cis	cerebellum	SCAN
rs7975632	OR6C70	trans	parietal	SCAN
rs7975632	PRPF40B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
6	chr12:48435400-48444600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:48435600-48444800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:48435600-48445800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:48435800-48444600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:48435800-48445800	Strong transcription	Primary B cells from cord blood	blood
12	chr12:48435800-48452400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:48436000-48445000	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:48436000-48445800	Strong transcription	Fetal Thymus	thymus
15	chr12:48436000-48448200	Strong transcription	Primary T cells from cord blood	blood
16	chr12:48436200-48444600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:48436200-48445800	Strong transcription	Dnd41	blood
18	chr12:48436400-48443400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:48436400-48443400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:48436400-48444000	Strong transcription	Fetal Lung	lung
21	chr12:48436400-48444200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:48436400-48444200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:48436400-48444200	Strong transcription	Brain Angular Gyrus	brain
24	chr12:48436400-48444600	Strong transcription	Placenta	Placenta
25	chr12:48436400-48444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:48436400-48445200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:48436600-48444600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:48436600-48445800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:48436800-48443800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:48436800-48444200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:48436800-48444600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:48437000-48443200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:48437000-48443400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:48437000-48443800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:48437000-48444400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:48437000-48444400	Strong transcription	Liver	Liver
37	chr12:48437000-48444400	Strong transcription	GM12878-XiMat	blood
38	chr12:48437000-48444600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:48437000-48444600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:48437000-48445400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:48437400-48444200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:48437400-48445200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:48437600-48443400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr12:48437600-48444600	Strong transcription	Adipose Nuclei	Adipose
46	chr12:48437800-48444800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:48437800-48444800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:48437800-48444800	Strong transcription	Thymus	Thymus
49	chr12:48437800-48446000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:48438200-48443200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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