Variant report

Variant	rs6296
Chromosome Location	chr6:78172260-78172261
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10806098	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662392	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13192352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000292	0.83[EUR][1000 genomes]
rs4142329	0.91[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs62416459	0.82[EUR][1000 genomes]
rs6298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916063	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6920728	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534282	chr6:77764575-78351994	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1015307	chr6:77902559-78352291	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1028259	chr6:78059491-78709871	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538325	chr6:78059491-78709871	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2758062	chr6:78100020-78283042	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2759445	chr6:78100020-78283042	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6296	IRAK1BP1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78169400-78174600	Active TSS	Aorta	Aorta
2	chr6:78171000-78172400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:78171400-78172600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:78171400-78172600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
5	chr6:78171400-78172800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
6	chr6:78171400-78173600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
7	chr6:78171400-78174400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:78171400-78174600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:78171400-78174600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
10	chr6:78171600-78172400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr6:78171600-78172400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
12	chr6:78171600-78172400	Bivalent/Poised TSS	Fetal Stomach	stomach
13	chr6:78171600-78172600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:78171600-78172600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:78171600-78172600	Active TSS	HMEC	breast
16	chr6:78171600-78172800	Bivalent/Poised TSS	NHLF	lung
17	chr6:78171600-78173000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:78171600-78174400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:78171600-78174600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:78171800-78172400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr6:78171800-78172400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
22	chr6:78171800-78172400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr6:78171800-78172400	Active TSS	Gastric	stomach
24	chr6:78171800-78172600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
25	chr6:78171800-78173800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr6:78171800-78174200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:78171800-78174400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:78171800-78174400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr6:78171800-78174800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr6:78171800-78174800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:78172000-78172400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:78172000-78172400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:78172000-78172400	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr6:78172000-78172400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:78172000-78172400	ZNF genes & repeats	Lung	lung
36	chr6:78172000-78172600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
37	chr6:78172000-78172600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:78172000-78172600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
39	chr6:78172000-78172600	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr6:78172000-78172600	Bivalent/Poised TSS	Fetal Heart	heart
41	chr6:78172000-78172600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr6:78172000-78172600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
43	chr6:78172000-78172600	Bivalent/Poised TSS	NHEK	skin
44	chr6:78172000-78172800	Active TSS	Right Ventricle	heart
45	chr6:78172000-78173000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:78172000-78173000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:78172000-78174200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:78172000-78174200	Active TSS	HUVEC	blood vessel
49	chr6:78172000-78174400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:78172200-78172400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood

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