Variant report

Variant	rs6689393
Chromosome Location	chr1:154426097-154426098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:154426074-154426358	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:154426056-154426421	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:154426088-154426412	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr1:154426021-154426477	U2OS	brain:	n/a	n/a
5	MYC	chr1:154426011-154426436	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr1:154426010-154426412	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:154425893-154426302	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:154426085-154426409	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr1:154426096-154426442	HepG2	liver:	n/a	n/a
10	FOS	chr1:154426046-154426438	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr1:154426094-154426285	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
IL6R	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10908838	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11265612	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12117832	0.81[AMR][1000 genomes]
rs12118770	0.87[AMR][1000 genomes]
rs12129500	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229238	0.83[ASW][hapmap]
rs4537545	0.94[ASW][hapmap];0.89[LWK][hapmap]
rs4553185	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4601580	0.86[JPT][hapmap]
rs4845371	0.94[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845618	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs4845619	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4845623	0.89[ASW][hapmap];0.80[LWK][hapmap]
rs4845625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59632925	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427658	0.88[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6667434	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6683206	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6686750	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689306	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6694258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694817	0.94[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7512646	0.80[AFR][1000 genomes]
rs7514452	0.83[ASW][hapmap]
rs7526131	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529229	0.94[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs7536152	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7549338	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553796	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6689393	PI4KB	cis	parietal	SCAN
rs6689393	UBAP2L	cis	parietal	SCAN
rs6689393	MYO9B	trans	cerebellum	SCAN
rs6689393	UBE2Q1	cis	cerebellum	SCAN
rs6689393	TMEM79	cis	parietal	SCAN
rs6689393	DENND4B	cis	cerebellum	SCAN
rs6689393	TDRD10	cis	lung	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154416200-154435800	Strong transcription	Liver	Liver
3	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:154418000-154428000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
6	chr1:154418600-154432800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr1:154419200-154427200	Weak transcription	Ovary	ovary
8	chr1:154419200-154432200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:154420800-154428000	Strong transcription	Colon Smooth Muscle	Colon
11	chr1:154421200-154426200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:154421200-154426200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:154421800-154431800	Strong transcription	Rectal Smooth Muscle	rectum
14	chr1:154422600-154434400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
16	chr1:154424200-154427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:154424400-154427800	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:154424600-154426600	Enhancers	NHDF-Ad	bronchial
19	chr1:154424800-154436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:154425000-154426400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:154425000-154426600	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr1:154425000-154429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
24	chr1:154425400-154426600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:154425600-154426200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:154425600-154426200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:154425600-154426400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:154425600-154426400	Enhancers	Brain Hippocampus Middle	brain
29	chr1:154425600-154426600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:154425600-154426600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:154425600-154426600	Enhancers	Fetal Muscle Leg	muscle
32	chr1:154425600-154426800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:154425600-154426800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:154425600-154426800	Enhancers	Osteobl	bone
35	chr1:154425600-154427000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:154425600-154427200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:154425600-154428200	Enhancers	Primary B cells from cord blood	blood
38	chr1:154425800-154426200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:154425800-154426200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:154425800-154426200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:154425800-154426200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:154425800-154426200	Genic enhancers	Gastric	stomach
43	chr1:154425800-154426200	Genic enhancers	Left Ventricle	heart
44	chr1:154425800-154426200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
45	chr1:154425800-154426200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:154425800-154426400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:154425800-154426400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:154425800-154426400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:154425800-154426400	Enhancers	Esophagus	oesophagus
50	chr1:154425800-154426400	Enhancers	Fetal Lung	lung

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