Variant report

Variant	rs6908105
Chromosome Location	chr6:79595097-79595098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11758432	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11964204	0.91[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12176511	0.90[ASN][1000 genomes]
rs12192086	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1338023	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2275290	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2275291	0.81[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs3805746	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3818839	0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3929867	0.86[ASN][1000 genomes]
rs7740307	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7750836	0.88[ASN][1000 genomes]
rs7756648	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7776138	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs9341753	0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9343849	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9343853	0.87[ASN][1000 genomes]
rs9343859	0.84[ASN][1000 genomes]
rs9343865	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9343867	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.81[ASN][1000 genomes]
rs9343869	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9350797	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs9350801	0.83[ASN][1000 genomes]
rs9352668	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9352672	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9352679	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9352685	0.81[ASN][1000 genomes]
rs9352688	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9359361	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9361459	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9361473	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap]
rs9361478	0.84[ASN][1000 genomes]
rs9361481	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs9361483	0.81[ASN][1000 genomes]
rs9443623	0.94[ASN][1000 genomes]
rs9448581	0.89[ASN][1000 genomes]
rs9448594	0.90[ASN][1000 genomes]
rs9448600	0.94[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9448601	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9448602	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9448616	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9688928	0.89[ASN][1000 genomes]

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	nsv1015352	chr6:79521820-79757024	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1839807	chr6:79532610-79606615	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6908105	IRAK1BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6908105	IRAK1BP1	cis	Nerve Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79577800-79597200	Weak transcription	Gastric	stomach
2	chr6:79578200-79597800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:79578200-79608600	Weak transcription	Adipose Nuclei	Adipose
4	chr6:79578200-79608600	Weak transcription	Left Ventricle	heart
5	chr6:79578200-79613600	Weak transcription	HSMM	muscle
6	chr6:79578400-79613800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:79578400-79619800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:79578400-79620000	Weak transcription	Right Ventricle	heart
9	chr6:79578600-79596000	Weak transcription	Fetal Heart	heart
10	chr6:79578600-79596600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:79578600-79598200	Weak transcription	HUVEC	blood vessel
12	chr6:79578600-79604800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:79578600-79612400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:79578600-79618200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:79578800-79602800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:79578800-79608600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:79578800-79613800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:79582000-79596600	Weak transcription	Ovary	ovary
19	chr6:79582000-79608400	Weak transcription	Fetal Intestine Large	intestine
20	chr6:79584800-79608600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:79585200-79619600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:79585200-79620200	Weak transcription	Fetal Lung	lung
23	chr6:79587600-79607600	Weak transcription	Dnd41	blood
24	chr6:79587600-79611200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:79587800-79608400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:79588000-79596200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:79588000-79596600	Weak transcription	Fetal Kidney	kidney
28	chr6:79588000-79619800	Weak transcription	Fetal Brain Female	brain
29	chr6:79588200-79598600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:79588200-79602000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:79588200-79611800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:79588200-79611800	Weak transcription	Pancreas	Pancrea
33	chr6:79588200-79612000	Weak transcription	Fetal Stomach	stomach
34	chr6:79588200-79616400	Weak transcription	Primary T cells from cord blood	blood
35	chr6:79588600-79597800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:79589600-79595600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:79589600-79596400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:79589600-79597000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:79589600-79600800	Weak transcription	Lung	lung
40	chr6:79589600-79618200	Weak transcription	Aorta	Aorta
41	chr6:79589600-79619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:79589800-79620200	Weak transcription	Fetal Brain Male	brain
43	chr6:79592600-79620200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:79593600-79596400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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