Variant report

Variant	rs4129267
Chromosome Location	chr1:154426264-154426265
allele	C/T
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	CEBPB	chr1:154426110-154426340	Hela-S3	cervix:	n/a	n/a
4	FOS	chr1:154426088-154426412	MCF10A-Er-Src	breast:	n/a	n/a
5	KAP1	chr1:154426021-154426477	U2OS	brain:	n/a	n/a
6	MYC	chr1:154426011-154426436	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:154426110-154426353	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr1:154426010-154426412	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:154426204-154426430	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr1:154425893-154426302	MCF10A-Er-Src	breast:	n/a	n/a
11	JUN	chr1:154426119-154426426	HepG2	liver:	n/a	chr1:154426271-154426284
12	CEBPB	chr1:154426101-154426322	IMR90	lung:	n/a	n/a
13	FOS	chr1:154426085-154426409	MCF10A-Er-Src	breast:	n/a	n/a
14	JUND	chr1:154426096-154426442	HepG2	liver:	n/a	n/a
15	FOS	chr1:154426046-154426438	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr1:154426121-154426396	MCF10A-Er-Src	breast:	n/a	n/a
17	JUND	chr1:154426243-154426375	K562	blood:	n/a	n/a
18	RUNX3	chr1:154426208-154426881	GM12878	blood:	n/a	n/a
19	MAX	chr1:154426094-154426285	Hela-S3	cervix:	n/a	n/a
20	RUNX3	chr1:154426117-154426882	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IL6R	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11265613	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126142	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133641	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730036	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730935	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753254	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393147	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4453032	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4537545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576655	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845372	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845373	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845620	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845621	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845622	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845623	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56383622	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61812598	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664201	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684439	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512646	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518199	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521458	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7529229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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

Variant related diseases (count:5)

Disease	PMID	Source
Pulmonary function	17903307	GWAS catalog
Asthma	21907864	GWAS catalog
C-reactive protein levels	21300955	GWAS catalog
Fibrinogen	23969696	GWAS catalog
Protein quantitative trait loci	18464913	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4129267	LINGO4	cis	parietal	SCAN
rs4129267	ANXA9	cis	parietal	SCAN
rs4129267	LYSMD1	cis	cerebellum	SCAN
rs4129267	GPATCH4	cis	cerebellum	SCAN

Chromatin state (count:100 , 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	chr1:154421800-154431800	Strong transcription	Rectal Smooth Muscle	rectum
12	chr1:154422600-154434400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
14	chr1:154424200-154427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:154424400-154427800	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:154424600-154426600	Enhancers	NHDF-Ad	bronchial
17	chr1:154424800-154436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:154425000-154426400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:154425000-154426600	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr1:154425000-154429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
22	chr1:154425400-154426600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:154425600-154426400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:154425600-154426400	Enhancers	Brain Hippocampus Middle	brain
25	chr1:154425600-154426600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:154425600-154426600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:154425600-154426600	Enhancers	Fetal Muscle Leg	muscle
28	chr1:154425600-154426800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:154425600-154426800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:154425600-154426800	Enhancers	Osteobl	bone
31	chr1:154425600-154427000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:154425600-154427200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:154425600-154428200	Enhancers	Primary B cells from cord blood	blood
34	chr1:154425800-154426400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:154425800-154426400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:154425800-154426400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:154425800-154426400	Enhancers	Esophagus	oesophagus
38	chr1:154425800-154426400	Enhancers	Fetal Lung	lung
39	chr1:154425800-154426400	Genic enhancers	Lung	lung
40	chr1:154425800-154426400	Enhancers	Psoas Muscle	Psoas
41	chr1:154425800-154426400	Genic enhancers	Stomach Mucosa	stomach
42	chr1:154425800-154426400	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr1:154425800-154426400	Genic enhancers	Spleen	Spleen
44	chr1:154425800-154426600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:154425800-154426600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:154425800-154426600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:154425800-154426600	Enhancers	Brain Anterior Caudate	brain
48	chr1:154425800-154426600	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr1:154425800-154426800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:154425800-154426800	Genic enhancers	Primary T cells from cord blood	blood

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