Variant report

Variant	rs12906480
Chromosome Location	chr15:31280093-31280094
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31279758..31282361-chr15:31424414..31426615,2	K562	blood:
2	chr15:31271252..31273468-chr15:31279975..31283092,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1133642	0.85[ASN][1000 genomes]
rs12437580	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439664	0.85[ASN][1000 genomes]
rs12443369	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914207	0.87[ASN][1000 genomes]
rs12914438	0.85[ASN][1000 genomes]
rs1404467	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404468	0.82[ASN][1000 genomes]
rs1404469	0.85[ASN][1000 genomes]
rs1404470	0.85[ASN][1000 genomes]
rs1425291	0.85[ASN][1000 genomes]
rs1524876	0.85[ASN][1000 genomes]
rs1880499	0.85[ASN][1000 genomes]
rs2140735	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272218	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272219	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293319	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293320	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339048	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28564430	0.82[ASN][1000 genomes]
rs2949572	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2949573	0.82[ASN][1000 genomes]
rs2949575	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2949576	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2949577	0.85[ASN][1000 genomes]
rs2949578	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2955783	0.85[ASN][1000 genomes]
rs2955787	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955791	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959047	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959049	0.85[ASN][1000 genomes]
rs2959050	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959051	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743231	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743233	0.82[ASN][1000 genomes]
rs4344701	0.83[ASN][1000 genomes]
rs71474640	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164530	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164939	0.83[ASN][1000 genomes]
rs7170710	0.85[ASN][1000 genomes]
rs7170772	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175256	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175951	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183880	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040989	0.80[ASN][1000 genomes]
rs8041717	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	87 gene(s)	inside rSNPs	diseases
8	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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 target site	28 gene(s)	inside rSNPs	diseases
9	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
10	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
12	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12906480	RP11-932O9.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31242000-31282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:31248800-31283000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:31250200-31282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:31250800-31282400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:31251200-31282400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:31251600-31282200	Weak transcription	Hela-S3	cervix
7	chr15:31252800-31282400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:31256000-31282400	Weak transcription	Fetal Brain Male	brain
9	chr15:31262200-31282200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:31267800-31282000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:31274800-31280400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:31275000-31281400	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr15:31275400-31280800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr15:31275600-31280200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:31276800-31280400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr15:31277000-31280600	Enhancers	Right Ventricle	heart
17	chr15:31277000-31282200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:31277200-31280200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:31277200-31280200	Strong transcription	Dnd41	blood
20	chr15:31277200-31280600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:31277200-31280600	Genic enhancers	Thymus	Thymus
22	chr15:31277200-31282200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:31277400-31280600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:31277400-31282200	Weak transcription	Brain Germinal Matrix	brain
25	chr15:31277600-31280200	Genic enhancers	Placenta	Placenta
26	chr15:31277600-31280600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:31277600-31282200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:31277800-31280400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr15:31277800-31280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:31277800-31280600	Genic enhancers	Brain Angular Gyrus	brain
31	chr15:31277800-31281400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:31277800-31282000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:31277800-31282000	Weak transcription	Ovary	ovary
34	chr15:31277800-31282400	Weak transcription	Fetal Brain Female	brain
35	chr15:31278000-31280600	Genic enhancers	Left Ventricle	heart
36	chr15:31278000-31281200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:31278200-31280200	Strong transcription	Primary B cells from cord blood	blood
38	chr15:31278200-31280200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:31278200-31280200	Weak transcription	Small Intestine	intestine
40	chr15:31278200-31280200	Weak transcription	GM12878-XiMat	blood
41	chr15:31278200-31280200	Weak transcription	HSMM	muscle
42	chr15:31278200-31280400	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:31278200-31280400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:31278200-31280600	Genic enhancers	Brain Cingulate Gyrus	brain
45	chr15:31278200-31281200	Weak transcription	NHDF-Ad	bronchial
46	chr15:31278200-31282200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:31278200-31282200	Weak transcription	HMEC	breast
48	chr15:31278200-31282200	Weak transcription	HSMMtube	muscle
49	chr15:31278200-31282200	Weak transcription	K562	blood
50	chr15:31278200-31283200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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