Variant report

Variant	rs1978161
Chromosome Location	chr12:48467721-48467722
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	chr12:48466511..48469101-chr12:48476522..48478242,2	K562	blood:
2	chr12:48459266..48462435-chr12:48465980..48469483,3	K562	blood:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1049392	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10747529	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875726	0.85[ASN][1000 genomes]
rs10875727	0.85[ASN][1000 genomes]
rs10875733	1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875739	1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs10875741	0.84[ASN][1000 genomes]
rs10875752	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10875754	0.82[JPT][hapmap]
rs10875761	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10875766	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs11168353	0.82[JPT][hapmap]
rs11168354	0.82[JPT][hapmap]
rs11168358	0.82[JPT][hapmap]
rs11168363	0.96[CHD][hapmap];0.82[JPT][hapmap]
rs11168364	0.96[CHD][hapmap];0.82[JPT][hapmap]
rs11168373	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168378	0.89[ASN][1000 genomes]
rs11168404	1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168417	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs11168424	0.81[JPT][hapmap]
rs11168434	0.82[JPT][hapmap]
rs11168435	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11168438	0.82[JPT][hapmap]
rs11168445	0.81[JPT][hapmap]
rs11168448	0.82[JPT][hapmap]
rs11168453	0.82[JPT][hapmap]
rs11168454	0.82[JPT][hapmap]
rs11832455	0.84[ASN][1000 genomes]
rs11834818	0.92[ASN][1000 genomes]
rs12422355	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12426981	0.92[ASN][1000 genomes]
rs17122567	0.82[JPT][hapmap]
rs1859440	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2107640	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158515	0.82[ASN][1000 genomes]
rs2240306	0.80[ASN][1000 genomes]
rs2286020	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2408954	0.82[JPT][hapmap]
rs3742075	0.92[ASN][1000 genomes]
rs3825403	1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4258439	0.96[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4760678	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56129148	0.87[ASN][1000 genomes]
rs7138917	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7299704	1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs7302354	0.82[JPT][hapmap]
rs7303677	1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7304428	0.84[ASN][1000 genomes]
rs733592	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7484942	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs765260	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7962390	0.82[JPT][hapmap]
rs7962569	0.88[JPT][hapmap]
rs8181670	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs886589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1978161	LOC255411	cis	cerebellum	SCAN
rs1978161	SENP1	cis	parietal	SCAN
rs1978161	PFKM	cis	parietal	SCAN
rs1978161	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
6	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:48444200-48474600	Weak transcription	Gastric	stomach
9	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
10	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:48452200-48468600	Strong transcription	NH-A	brain
15	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
19	chr12:48452400-48468800	Strong transcription	Adipose Nuclei	Adipose
20	chr12:48452400-48468800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:48452400-48468800	Strong transcription	Fetal Thymus	thymus
22	chr12:48452400-48469600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:48452600-48468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:48452800-48468000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:48452800-48468600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:48453000-48468400	Strong transcription	Fetal Lung	lung
27	chr12:48453000-48468800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:48453000-48469200	Weak transcription	Fetal Heart	heart
29	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:48453200-48469200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr12:48453600-48469800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:48453600-48471200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:48453800-48469000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:48453800-48469000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:48453800-48469000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:48453800-48469000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:48453800-48469400	Strong transcription	A549	lung
38	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:48454000-48469000	Strong transcription	Liver	Liver
40	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:48454600-48469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
43	chr12:48454800-48472000	Strong transcription	Dnd41	blood
44	chr12:48455600-48469000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:48456200-48469600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
47	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
48	chr12:48459200-48467800	Weak transcription	NHLF	lung
49	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:48460800-48468200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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