Variant report

Variant	rs10456
Chromosome Location	chr15:78398146-78398147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78298725..78300979-chr15:78395838..78398547,2	K562	blood:
2	chr15:78394209..78398078-chr15:78398123..78400882,3	MCF-7	breast:
3	chr15:78392111..78393882-chr15:78397751..78399759,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11072727	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11072728	0.87[CEU][hapmap];0.84[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11072729	0.87[CEU][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11856461	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438507	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441722	1.00[ASN][1000 genomes]
rs17479031	1.00[CHB][hapmap]
rs17479135	1.00[CHB][hapmap]
rs17850484	1.00[CHB][hapmap]
rs2304829	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs3825847	1.00[CHB][hapmap]
rs59999498	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62009271	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62009273	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495273	0.90[CEU][hapmap]
rs7164338	0.87[CEU][hapmap];0.85[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7165154	1.00[CHB][hapmap]
rs7182113	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv274890	chr15:78396447-78402258	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10456	CIB2	cis	lymphoblastoid	seeQTL
rs10456	UBE2Q2	cis	parietal	SCAN
rs10456	ULK3	cis	parietal	SCAN
rs10456	RP11-114H24.2	cis	Muscle Skeletal	GTEx
rs10456	IREB2	cis	cerebellum	SCAN
rs10456	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs10456	CIB2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78385200-78400600	Weak transcription	Pancreas	Pancrea
2	chr15:78392000-78400600	Strong transcription	Thymus	Thymus
3	chr15:78393200-78406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78393400-78401200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:78393800-78399200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr15:78394200-78399200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:78394600-78398600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr15:78394600-78398800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr15:78394800-78398600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr15:78394800-78398600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr15:78394800-78398800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:78394800-78398800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:78394800-78398800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:78394800-78399000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr15:78395000-78398600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:78395000-78398800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr15:78395000-78405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:78395200-78398200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr15:78395200-78398400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:78395200-78398600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:78395200-78398600	Genic enhancers	Fetal Thymus	thymus
22	chr15:78395200-78399000	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:78395400-78398600	Enhancers	Spleen	Spleen
24	chr15:78395400-78405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:78395600-78398800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr15:78395600-78399200	Genic enhancers	Fetal Intestine Small	intestine
27	chr15:78395800-78398400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:78395800-78398400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:78395800-78398600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:78395800-78400200	Strong transcription	Fetal Brain Female	brain
31	chr15:78396000-78400000	Strong transcription	Brain Germinal Matrix	brain
32	chr15:78396000-78405400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:78396200-78398400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:78396200-78398400	Weak transcription	Stomach Mucosa	stomach
35	chr15:78396200-78398600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:78396200-78399000	Enhancers	GM12878-XiMat	blood
37	chr15:78396200-78399200	Enhancers	Placenta	Placenta
38	chr15:78396200-78400600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:78396200-78400600	Weak transcription	Right Atrium	heart
40	chr15:78396200-78405600	Weak transcription	Brain Anterior Caudate	brain
41	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
42	chr15:78396400-78398600	Enhancers	Primary T cells from cord blood	blood
43	chr15:78396400-78404000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:78396400-78405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:78396600-78398200	Weak transcription	HSMM	muscle
46	chr15:78396600-78398600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:78396600-78405400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:78396600-78405600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:78396800-78399000	Genic enhancers	Fetal Intestine Large	intestine

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