Variant report

Variant	rs12297004
Chromosome Location	chr12:48453820-48453821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48435313..48437988-chr12:48451982..48454529,2	K562	blood:
2	chr12:48438521..48441289-chr12:48453663..48455764,2	K562	blood:
3	chr12:48404615..48406562-chr12:48453440..48456086,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258203	Chromatin interaction
ENSG00000257985	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10219623	0.85[AMR][1000 genomes]
rs10875725	0.82[ASN][1000 genomes]
rs10875728	0.80[EUR][1000 genomes]
rs10875729	0.80[EUR][1000 genomes]
rs10875730	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875731	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875732	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875738	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875745	0.85[AMR][1000 genomes]
rs10875746	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10875747	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875748	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875750	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875756	0.81[EUR][1000 genomes]
rs11168369	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168370	0.83[EUR][1000 genomes]
rs11168371	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168374	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168386	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168413	0.85[AMR][1000 genomes]
rs11168414	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168418	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168420	0.90[EUR][1000 genomes]
rs11168422	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168427	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168433	0.81[EUR][1000 genomes]
rs12296244	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12297470	0.85[AMR][1000 genomes]
rs12301339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12304476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12306451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12310813	0.85[AMR][1000 genomes]
rs12310999	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12315625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122666	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1859445	0.85[AMR][1000 genomes]
rs2107638	0.85[AMR][1000 genomes]
rs2158516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228500	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2269935	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2269936	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286021	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3782910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760681	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4760689	0.81[EUR][1000 genomes]
rs4760690	0.81[EUR][1000 genomes]
rs58952582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60761335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918774	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61918806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61918809	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61918810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725454	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73102065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73102067	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485355	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8804	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs886588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs989144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12297004	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12297004	RP1-228P16.1	cis	Thyroid	GTEx
rs12297004	RP1-228P16.1	cis	Artery Tibial	GTEx
rs12297004	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs12297004	RP1-228P16.1	cis	Adipose Subcutaneous	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	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
5	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48439200-48456800	Weak transcription	HMEC	breast
8	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
10	chr12:48440000-48454000	Weak transcription	HUVEC	blood vessel
11	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:48441200-48457000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:48441400-48454400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
15	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:48444200-48474600	Weak transcription	Gastric	stomach
18	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
19	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:48452000-48460200	Strong transcription	Hela-S3	cervix
21	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:48452200-48454000	ZNF genes & repeats	GM12878-XiMat	blood
26	chr12:48452200-48454200	Strong transcription	Brain Substantia Nigra	brain
27	chr12:48452200-48454600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:48452200-48454800	ZNF genes & repeats	Dnd41	blood
29	chr12:48452200-48455200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:48452200-48459600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:48452200-48459600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:48452200-48459600	Strong transcription	NHDF-Ad	bronchial
33	chr12:48452200-48460000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:48452200-48460600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:48452200-48461200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:48452200-48461600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:48452200-48468600	Strong transcription	NH-A	brain
38	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
42	chr12:48452400-48454000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr12:48452400-48454000	ZNF genes & repeats	Liver	Liver
44	chr12:48452400-48454000	ZNF genes & repeats	Thymus	Thymus
45	chr12:48452400-48454000	Strong transcription	HSMMtube	muscle
46	chr12:48452400-48454200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr12:48452400-48454400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:48452400-48455200	ZNF genes & repeats	Primary B cells from cord blood	blood
49	chr12:48452400-48459400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:48452400-48459600	Strong transcription	Rectal Mucosa Donor 29	rectum

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