Variant report

Variant	rs7299704
Chromosome Location	chr12:48444488-48444489
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: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10492082	0.89[ASN][1000 genomes]
rs1049392	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10747529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875726	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875727	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875733	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875739	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];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875741	0.86[EUR][1000 genomes]
rs10875744	0.85[EUR][1000 genomes]
rs10875752	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875754	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10875761	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875766	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168361	0.86[ASN][1000 genomes]
rs11168363	0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168364	0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168373	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168378	0.81[ASN][1000 genomes]
rs11168404	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11168417	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11168424	1.00[JPT][hapmap]
rs11168434	1.00[JPT][hapmap]
rs11168435	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11168438	1.00[JPT][hapmap]
rs11168445	1.00[JPT][hapmap]
rs11168448	1.00[JPT][hapmap]
rs11168453	1.00[JPT][hapmap]
rs11168454	1.00[JPT][hapmap]
rs11832455	0.83[EUR][1000 genomes]
rs11834818	0.85[ASN][1000 genomes]
rs12422355	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12426981	0.85[ASN][1000 genomes]
rs17122567	1.00[JPT][hapmap]
rs1859440	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1859443	0.94[JPT][hapmap]
rs1978161	1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs2056448	0.84[ASN][1000 genomes]
rs2107640	0.82[ASN][1000 genomes]
rs2158515	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2240306	0.90[ASN][1000 genomes]
rs2286020	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2408954	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3742075	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs3825403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4258439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760678	0.84[ASN][1000 genomes]
rs56129148	0.86[EUR][1000 genomes]
rs59667534	0.89[ASN][1000 genomes]
rs6580658	0.80[JPT][hapmap]
rs7138917	0.96[CEU][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302354	1.00[JPT][hapmap]
rs7303677	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7304428	0.86[EUR][1000 genomes]
rs733592	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7484942	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs765260	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7962390	1.00[JPT][hapmap]
rs7962569	0.94[JPT][hapmap]
rs8181670	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs886589	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs954326	0.94[JPT][hapmap]
rs9651981	0.94[JPT][hapmap]
rs9804751	0.94[JPT][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7299704	RP1-228P16.1	cis	Thyroid	GTEx
rs7299704	RPAP3	cis	cerebellum	SCAN
rs7299704	C12orf41	cis	parietal	SCAN
rs7299704	SENP1	cis	parietal	SCAN
rs7299704	ZNF641	cis	Whole Blood	GTEx
rs7299704	RP1-228P16.1	cis	Esophagus Muscularis	GTEx
rs7299704	RP1-228P16.1	cis	Artery Tibial	GTEx

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	chr12:48436400-48444600	Strong transcription	Placenta	Placenta
19	chr12:48436400-48444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:48436400-48445200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:48436600-48444600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:48436600-48445800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:48436800-48444600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:48437000-48444600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:48437000-48444600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:48437000-48445400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:48437400-48445200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:48437600-48444600	Strong transcription	Adipose Nuclei	Adipose
30	chr12:48437800-48444800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:48437800-48444800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr12:48437800-48444800	Strong transcription	Thymus	Thymus
33	chr12:48437800-48446000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:48438200-48445000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:48439200-48444600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:48439200-48448200	Weak transcription	HSMMtube	muscle
37	chr12:48439200-48448800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:48439200-48448800	Weak transcription	Pancreas	Pancrea
39	chr12:48439200-48453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:48439200-48456800	Weak transcription	HMEC	breast
41	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:48439400-48445200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
44	chr12:48440000-48452200	Weak transcription	NHDF-Ad	bronchial
45	chr12:48440000-48454000	Weak transcription	HUVEC	blood vessel
46	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:48440200-48444600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:48440200-48452600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:48440200-48452600	Weak transcription	Right Ventricle	heart
50	chr12:48440200-48453800	Weak transcription	Colon Smooth Muscle	Colon

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