Variant report

Variant	rs6936706
Chromosome Location	chr6:58269738-58269739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10789525	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12213747	0.85[ASN][1000 genomes]
rs13777	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15680	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1810425	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1810426	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049928	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049929	0.83[AMR][1000 genomes]
rs2758435	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28397909	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3864247	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3895119	0.87[ASN][1000 genomes]
rs3996599	0.89[AFR][1000 genomes]
rs4469327	0.94[AFR][1000 genomes]
rs477994	0.85[ASN][1000 genomes]
rs4928320	0.84[ASN][1000 genomes]
rs4928324	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4928423	0.87[ASN][1000 genomes]
rs4928424	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4928425	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4928426	0.82[ASN][1000 genomes]
rs508070	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs512604	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6588681	0.87[ASN][1000 genomes]
rs6931014	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7749396	0.84[ASN][1000 genomes]
rs7765285	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326195	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9326196	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9404713	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9500243	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9500250	0.84[ASN][1000 genomes]
rs9500251	0.83[ASN][1000 genomes]
rs9766482	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv436517	chr6:57696174-58296165	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3332363	chr6:57709182-58454441	Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3426791	chr6:57741382-58349943	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3440047	chr6:57766598-58396144	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3372144	chr6:57908014-58519523	Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv435830	chr6:57912721-58515824	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3503622	chr6:57916040-58522258	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3503623	chr6:57916040-58522258	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	esv3445656	chr6:57975137-58576488	Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv821647	chr6:58067314-58678227	Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv869817	chr6:58071721-58614002	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv885965	chr6:58075480-58308955	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv523720	chr6:58075480-58770624	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1024377	chr6:58082084-58774716	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv428148	chr6:58137660-58406917	Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1020262	chr6:58140288-58774716	ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv2760987	chr6:58140300-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv1029158	chr6:58142069-58759016	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv1017058	chr6:58165571-58774716	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv1026793	chr6:58181781-58422630	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv538259	chr6:58182242-58656519	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1019643	chr6:58213416-58350871	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv1029598	chr6:58213416-58358630	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1030059	chr6:58222882-58377586	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv603237	chr6:58231219-58780055	Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
26	nsv885966	chr6:58238236-58333290	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
27	nsv7906	chr6:58243673-58270073	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
28	esv13110	chr6:58244095-58274338	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv1024304	chr6:58249544-58377586	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	esv3422773	chr6:58264493-58270291	Weak transcription Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
31	nsv969409	chr6:58266198-58398028	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6936706	LINC00680	cis	Stomach	GTEx
rs6936706	LINC00680	cis	Nerve Tibial	GTEx
rs6936706	LINC00680	cis	lung	GTEx
rs6936706	GUSBL2	Cis_1M	lymphoblastoid	RTeQTL
rs6936706	LINC00680	cis	Skin Sun Exposed Lower leg	GTEx
rs6936706	LINC00680	cis	Esophagus Mucosa	GTEx
rs6936706	LINC00680	cis	Adipose Subcutaneous	GTEx
rs6936706	XXbac-BPGBPG55C20.2	cis	Esophagus Muscularis	GTEx
rs6936706	LINC00680	cis	Thyroid	GTEx
rs6936706	LINC00680	cis	Esophagus Muscularis	GTEx
rs6936706	LINC00680	cis	Artery Tibial	GTEx
rs6936706	LINC00680	cis	Muscle Skeletal	GTEx
rs6936706	LINC00680	cis	Artery Aorta	GTEx
rs6936706	GUSBP4	cis	Nerve Tibial	GTEx
rs6936706	LINC00680	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:58243000-58272800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:58244000-58272400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:58244200-58287200	Weak transcription	Right Ventricle	heart
4	chr6:58244400-58272600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:58244800-58273000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:58245800-58272400	Weak transcription	Fetal Brain Female	brain
7	chr6:58245800-58272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:58245800-58275000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:58247200-58272400	Weak transcription	Left Ventricle	heart
10	chr6:58247200-58273200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:58248800-58272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:58250800-58272400	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:58250800-58275000	Weak transcription	Gastric	stomach
14	chr6:58250800-58287200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:58251000-58272400	Weak transcription	Spleen	Spleen
16	chr6:58251200-58272400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:58251200-58272400	Weak transcription	Liver	Liver
18	chr6:58255200-58272400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:58261400-58286600	Weak transcription	Brain Germinal Matrix	brain
20	chr6:58264200-58272600	Weak transcription	Fetal Stomach	stomach
21	chr6:58265400-58272400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:58267400-58272600	Weak transcription	Aorta	Aorta
23	chr6:58267600-58272400	Weak transcription	Thymus	Thymus
24	chr6:58267800-58273000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:58268200-58272400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:58268200-58272400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:58268200-58272800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:58268600-58274800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:58269400-58272400	Weak transcription	Adipose Nuclei	Adipose
30	chr6:58269600-58272000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:58269600-58273000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:58269600-58273000	Weak transcription	Dnd41	blood

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