Variant report

Variant	rs9969480
Chromosome Location	chr8:125274252-125274253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125162472..125164935-chr8:125272607..125274873,2	MCF-7	breast:
2	chr8:125049009..125051707-chr8:125273517..125275708,2	MCF-7	breast:
3	chr8:125273484..125276342-chr8:125277791..125281041,4	K562	blood:
4	chr8:125273657..125275518-chr8:125282049..125285179,3	MCF-7	breast:
5	chr8:125274009..125276949-chr8:125383546..125386105,3	MCF-7	breast:
6	chr17:57920811..57923006-chr8:125273669..125275366,2	MCF-7	breast:
7	chr8:125273998..125276342-chr8:125277688..125279573,2	K562	blood:

Variant related genes	Relation type
ENSG00000253885	Chromatin interaction
ENSG00000164983	Chromatin interaction
ENSG00000253227	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10087001	0.80[ASN][1000 genomes]
rs10087062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10087137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10087222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10087374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10091808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10092616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13439237	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13439439	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13439443	0.81[CHB][hapmap]
rs16899475	0.95[CHB][hapmap]
rs17295226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17295548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17360690	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs17360711	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17360746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17360788	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4360277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4374970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4504618	1.00[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4593526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4871476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4871477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4871478	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4871480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4871481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4871482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55784871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945711	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56068026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56218959	0.82[ASN][1000 genomes]
rs56383080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60167901	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60995425	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66467223	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66961607	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67153514	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67712436	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67815046	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68047305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6983392	0.83[ASN][1000 genomes]
rs6984141	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6984458	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6984642	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6984921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6986310	0.87[EUR][1000 genomes]
rs6988141	0.82[ASN][1000 genomes]
rs7003238	0.83[ASN][1000 genomes]
rs7003974	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7011052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7011213	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7011528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72719397	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73345158	0.80[ASN][1000 genomes]
rs73345172	0.82[ASN][1000 genomes]
rs73345176	0.80[ASN][1000 genomes]
rs7842882	0.92[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9297691	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9297693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969479	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9969480	RP11-383J24.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125258400-125282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:125271200-125274600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr8:125272600-125277200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:125272800-125277400	Enhancers	Primary B cells from peripheral blood	blood
5	chr8:125273000-125277000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr8:125273400-125274600	Flanking Active TSS	Hela-S3	cervix
7	chr8:125273400-125275600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr8:125273400-125275600	Enhancers	Fetal Intestine Large	intestine
9	chr8:125273400-125275600	Enhancers	Thymus	Thymus
10	chr8:125273400-125275800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:125273400-125275800	Enhancers	Primary hematopoietic stem cells	blood
12	chr8:125273400-125275800	Enhancers	Fetal Intestine Small	intestine
13	chr8:125273400-125276000	Enhancers	HUVEC	blood vessel
14	chr8:125273400-125276400	Enhancers	Dnd41	blood
15	chr8:125273400-125276800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:125273600-125274400	Weak transcription	Gastric	stomach
17	chr8:125273600-125275600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:125273600-125275600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr8:125273600-125275600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr8:125273600-125275600	Enhancers	GM12878-XiMat	blood
21	chr8:125273600-125275800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr8:125273600-125275800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr8:125273600-125275800	Enhancers	Fetal Thymus	thymus
24	chr8:125273600-125276000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr8:125273600-125276200	Enhancers	Primary B cells from cord blood	blood
26	chr8:125273800-125274600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:125273800-125274600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:125273800-125274600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr8:125273800-125274600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:125273800-125274600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:125273800-125274600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr8:125273800-125274600	Enhancers	NHEK	skin
33	chr8:125273800-125274800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr8:125273800-125274800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr8:125273800-125275000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr8:125273800-125275000	Flanking Active TSS	A549	lung
37	chr8:125273800-125275200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr8:125273800-125275200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:125273800-125275400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:125273800-125275400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:125273800-125275400	Enhancers	Fetal Muscle Leg	muscle
42	chr8:125273800-125275400	Enhancers	Left Ventricle	heart
43	chr8:125273800-125275400	Enhancers	Lung	lung
44	chr8:125273800-125275400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr8:125273800-125275400	Enhancers	Spleen	Spleen
46	chr8:125273800-125275400	Enhancers	NH-A	brain
47	chr8:125273800-125275400	Enhancers	Osteobl	bone
48	chr8:125273800-125275600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr8:125273800-125275600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr8:125273800-125275600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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