Variant report

Variant	rs4712936
Chromosome Location	chr6:25417423-25417424
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2039069	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34991172	0.80[EUR][1000 genomes]
rs4632883	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7752195	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7774567	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs913455	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9295661	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4712936	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4712936	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 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	chr6:25409000-25419000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:25411600-25418200	Weak transcription	Lung	lung
6	chr6:25412800-25417800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:25412800-25417800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:25413000-25417800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:25413000-25417800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:25413200-25418000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:25414000-25418200	Weak transcription	Stomach Mucosa	stomach
12	chr6:25414400-25418600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:25414400-25419800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:25414600-25418000	Enhancers	Aorta	Aorta
15	chr6:25414600-25419400	Enhancers	Fetal Lung	lung
16	chr6:25414600-25420400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:25414600-25423600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:25414800-25420200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:25414800-25420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:25415200-25419000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:25415200-25419400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:25415200-25420400	Weak transcription	Primary T cells from cord blood	blood
24	chr6:25415200-25431800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:25415600-25417600	Weak transcription	Left Ventricle	heart
26	chr6:25415600-25419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:25415600-25419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25415600-25420000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:25415600-25421000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:25415600-25422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:25415600-25424000	Weak transcription	Thymus	Thymus
32	chr6:25415800-25418800	Enhancers	Ovary	ovary
33	chr6:25416000-25418800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:25416200-25417600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:25416200-25420200	Enhancers	Fetal Intestine Large	intestine
36	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
37	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
38	chr6:25416400-25417800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:25416400-25418200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:25416400-25418600	Weak transcription	Right Atrium	heart
41	chr6:25416600-25417600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:25416600-25427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:25416800-25417600	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:25416800-25418200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:25416800-25419800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:25416800-25420000	Enhancers	Fetal Intestine Small	intestine
48	chr6:25417000-25417600	Enhancers	Duodenum Mucosa	Duodenum
49	chr6:25417000-25417600	Enhancers	Fetal Kidney	kidney
50	chr6:25417000-25417800	Enhancers	Cortex derived primary cultured neurospheres	brain

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