Variant report

Variant	rs7304428
Chromosome Location	chr12:48494275-48494276
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48485766..48487842-chr12:48492763..48495149,2	MCF-7	breast:
2	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
3	chr12:48493205..48495553-chr12:48549427..48551502,2	MCF-7	breast:
4	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1049392	0.91[ASN][1000 genomes]
rs10747529	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875726	0.83[EUR][1000 genomes]
rs10875727	0.84[EUR][1000 genomes]
rs10875739	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875741	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875744	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875754	0.80[ASN][1000 genomes]
rs11168404	0.89[ASN][1000 genomes]
rs11168412	0.91[ASN][1000 genomes]
rs11168417	0.87[ASN][1000 genomes]
rs11168419	0.87[ASN][1000 genomes]
rs11168424	0.89[ASN][1000 genomes]
rs11832455	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12228924	0.91[ASN][1000 genomes]
rs12425679	0.87[ASN][1000 genomes]
rs1978161	0.84[ASN][1000 genomes]
rs2107640	0.92[ASN][1000 genomes]
rs2158515	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286020	0.87[ASN][1000 genomes]
rs3825403	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4258439	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760678	0.82[ASN][1000 genomes]
rs56129148	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57430775	0.87[ASN][1000 genomes]
rs58540891	0.91[ASN][1000 genomes]
rs58556309	0.87[ASN][1000 genomes]
rs7138917	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7299704	0.86[EUR][1000 genomes]
rs7302354	0.91[ASN][1000 genomes]
rs7303677	0.86[ASN][1000 genomes]
rs73104071	0.91[ASN][1000 genomes]
rs886589	0.80[AMR][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	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
2	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
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7304428	RP1-228P16.1	cis	Thyroid	GTEx
rs7304428	RP1-228P16.1	cis	Artery Tibial	GTEx
rs7304428	RP1-228P16.1	cis	Esophagus Muscularis	GTEx
rs7304428	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:123 , 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	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
6	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:48473600-48495400	Strong transcription	Dnd41	blood
8	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
10	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
11	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
15	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
16	chr12:48479600-48498000	Weak transcription	NHEK	skin
17	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:48482800-48498200	Weak transcription	NHDF-Ad	bronchial
19	chr12:48483000-48498200	Weak transcription	NH-A	brain
20	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
21	chr12:48483200-48498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:48483200-48498200	Weak transcription	HepG2	liver
23	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
25	chr12:48483400-48498200	Weak transcription	NHLF	lung
26	chr12:48484800-48498200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:48485000-48498200	Weak transcription	Spleen	Spleen
28	chr12:48486200-48499000	Weak transcription	Gastric	stomach
29	chr12:48486400-48497800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:48487200-48494400	Strong transcription	Fetal Stomach	stomach
31	chr12:48488000-48496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:48488000-48498200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:48488200-48495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:48488200-48497600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:48488200-48498200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:48488200-48498200	Weak transcription	Lung	lung
37	chr12:48488200-48498200	Weak transcription	Pancreas	Pancrea
38	chr12:48488200-48498400	Weak transcription	Brain Substantia Nigra	brain
39	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:48488400-48494800	Strong transcription	Hela-S3	cervix
41	chr12:48488400-48498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:48488400-48498400	Weak transcription	Right Ventricle	heart
43	chr12:48489000-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:48489600-48497200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:48489600-48498400	Weak transcription	Left Ventricle	heart
46	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
47	chr12:48489800-48498200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:48489800-48498200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:48489800-48498200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:48489800-48498400	Weak transcription	Thymus	Thymus

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