Variant report

Variant	rs9295661
Chromosome Location	chr6:25450026-25450027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25448709..25450289-chr6:25450958..25453403,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1028885	1.00[YRI][hapmap]
rs2039069	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2769703	0.82[LWK][hapmap]
rs301400	0.83[AMR][1000 genomes]
rs34991172	0.82[EUR][1000 genomes]
rs4632883	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4712936	0.93[EUR][1000 genomes]
rs6900224	1.00[YRI][hapmap]
rs7752195	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7774567	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs913455	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3406200	chr6:25449998-25452546	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9295661	BTN3A2	cis	multi-tissue	Pritchard
rs9295661	HLA-A	cis	multi-tissue	Pritchard
rs9295661	BTN3A2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25418800-25462600	Weak transcription	Ovary	ovary
3	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:25434200-25450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:25442000-25455600	Weak transcription	Aorta	Aorta
8	chr6:25443200-25472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:25446600-25460000	Weak transcription	Fetal Lung	lung
10	chr6:25446800-25450200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:25446800-25450800	Enhancers	HMEC	breast
12	chr6:25446800-25451000	Enhancers	NHEK	skin
13	chr6:25446800-25451400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:25446800-25454200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:25446800-25454200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:25446800-25493600	Weak transcription	Left Ventricle	heart
17	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
18	chr6:25447000-25450600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:25447000-25450800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:25447000-25450800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25447000-25451600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:25447400-25452200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:25447400-25473200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:25447800-25450800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:25447800-25453800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:25448000-25450200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:25448000-25450200	Weak transcription	Stomach Mucosa	stomach
28	chr6:25448000-25450800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:25448000-25451600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:25448200-25450800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:25448200-25451600	Weak transcription	Right Atrium	heart
32	chr6:25448200-25472600	Weak transcription	Pancreas	Pancrea
33	chr6:25448400-25456600	Weak transcription	Gastric	stomach
34	chr6:25448400-25464400	Weak transcription	Thymus	Thymus
35	chr6:25448600-25450200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:25448600-25450800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:25448800-25450600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:25448800-25451000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr6:25449000-25451000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:25449000-25462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:25449000-25463600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:25449200-25450400	Enhancers	Fetal Brain Female	brain
43	chr6:25449200-25450800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:25449200-25454000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:25449400-25450400	Enhancers	GM12878-XiMat	blood
46	chr6:25449400-25450800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr6:25449400-25450800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:25449400-25450800	Enhancers	Brain Substantia Nigra	brain
49	chr6:25449400-25451800	Weak transcription	Fetal Intestine Small	intestine
50	chr6:25449400-25515800	Weak transcription	Lung	lung

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