Variant report

Variant	rs7752195
Chromosome Location	chr6:25419094-25419095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25409840..25412613-chr6:25418004..25420137,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2039069	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2328887	0.90[AFR][1000 genomes]
rs34991172	0.80[EUR][1000 genomes]
rs4632883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4712936	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7774567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs913455	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9295661	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7752195	BTN3A2	cis	lymphoblastoid	seeQTL
rs7752195	HLA-A	cis	multi-tissue	Pritchard
rs7752195	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs7752195	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7752195	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25406400-25420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:25407200-25420200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:25414400-25419800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:25414600-25419400	Enhancers	Fetal Lung	lung
6	chr6:25414600-25420400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:25414600-25423600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:25414800-25420200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:25414800-25420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:25415200-25419400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:25415200-25420400	Weak transcription	Primary T cells from cord blood	blood
13	chr6:25415200-25431800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:25415600-25419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:25415600-25419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:25415600-25420000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:25415600-25421000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:25415600-25422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25415600-25424000	Weak transcription	Thymus	Thymus
20	chr6:25416200-25420200	Enhancers	Fetal Intestine Large	intestine
21	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
22	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
23	chr6:25416600-25427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:25416800-25419800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:25416800-25420000	Enhancers	Fetal Intestine Small	intestine
27	chr6:25417000-25419600	Enhancers	Osteobl	bone
28	chr6:25417600-25419400	Enhancers	Left Ventricle	heart
29	chr6:25417600-25419600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:25417600-25431800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:25417800-25419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:25417800-25419400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:25417800-25419600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:25417800-25419800	Enhancers	Small Intestine	intestine
35	chr6:25417800-25420200	Weak transcription	Primary B cells from cord blood	blood
36	chr6:25418000-25421200	Weak transcription	Liver	Liver
37	chr6:25418000-25429200	Weak transcription	Aorta	Aorta
38	chr6:25418200-25419400	Enhancers	Lung	lung
39	chr6:25418200-25419400	Enhancers	Stomach Mucosa	stomach
40	chr6:25418400-25420800	Weak transcription	Brain Substantia Nigra	brain
41	chr6:25418400-25422000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:25418600-25419400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:25418600-25420400	Enhancers	Right Atrium	heart
44	chr6:25418600-25426200	Weak transcription	Gastric	stomach
45	chr6:25418800-25419600	Flanking Active TSS	Hela-S3	cervix
46	chr6:25418800-25420200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:25418800-25420400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:25418800-25420400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:25418800-25421600	Weak transcription	Adipose Nuclei	Adipose
50	chr6:25418800-25462600	Weak transcription	Ovary	ovary

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