Variant report

Variant	rs11208930
Chromosome Location	chr1:67090034-67090035
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	EP300	chr1:67089251-67090660	SK-N-SH	brain:	n/a	chr1:67089659-67089668 chr1:67090268-67090277
2	GATA3	chr1:67089286-67091505	SK-N-SH	brain:	n/a	chr1:67090266-67090275 chr1:67089763-67089773 chr1:67089657-67089667 chr1:67089421-67089430 chr1:67090596-67090604
3	FOSL2	chr1:67089330-67090615	SK-N-SH	brain:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
4	JUND	chr1:67090029-67090618	HCT-116	colon:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
5	TCF12	chr1:67089279-67090749	SK-N-SH	brain:	n/a	n/a
6	KAP1	chr1:67089361-67090411	U2OS	brain:	n/a	chr1:67089885-67089893
7	JUND	chr1:67089306-67090665	SK-N-SH	brain:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
8	FOS	chr1:67089896-67090536	MCF10A-Er-Src	breast:	n/a	chr1:67090294-67090305 chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090266-67090277 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
9	MYC	chr1:67090031-67090521	MCF10A-Er-Src	breast:	n/a	n/a
10	FOSL1	chr1:67089944-67090625	HCT-116	colon:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
11	TCF12	chr1:67089226-67090747	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr1:67089943-67090463	SK-N-SH	brain:	n/a	n/a
13	JUND	chr1:67090025-67090582	HCT-116	colon:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
14	POLR2A	chr1:67090027-67090532	SK-N-SH	brain:	n/a	n/a
15	EP300	chr1:67089208-67091520	SK-N-SH	brain:	n/a	chr1:67089659-67089668 chr1:67090268-67090277
16	NFIC	chr1:67089282-67090645	SK-N-SH	brain:	n/a	chr1:67089600-67089617 chr1:67089600-67089616
17	PBX3	chr1:67089443-67090832	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr1:67089308-67090684	SK-N-SH	brain:	n/a	chr1:67090266-67090275 chr1:67089763-67089773 chr1:67089657-67089667 chr1:67089421-67089430 chr1:67090596-67090604
19	FOS	chr1:67089845-67090534	MCF10A-Er-Src	breast:	n/a	chr1:67090294-67090305 chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090266-67090277 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277
20	EP300	chr1:67089453-67090661	SK-N-SH	brain:	n/a	chr1:67089659-67089668 chr1:67090268-67090277
21	JUND	chr1:67089343-67090699	SK-N-SH	brain:	n/a	chr1:67090295-67090305 chr1:67090266-67090278 chr1:67090268-67090276 chr1:67090294-67090306 chr1:67090268-67090275 chr1:67090296-67090304 chr1:67090267-67090277 chr1:67090268-67090276 chr1:67090267-67090277

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67088339..67090517-chr1:67091923..67094068,2	K562	blood:

Variant related genes	Relation type
SGIP1	TF binding region
MIR3117	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10493411	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs10789211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889638	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208910	1.00[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs11208916	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208924	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11208929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208937	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs12021913	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12023176	0.80[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12031054	0.85[YRI][hapmap]
rs12034344	0.92[EUR][1000 genomes]
rs12039282	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046520	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12093843	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12402181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565798	0.86[EUR][1000 genomes]
rs12567556	0.92[EUR][1000 genomes]
rs1359461	0.89[YRI][hapmap]
rs1373909	0.86[JPT][hapmap]
rs17129039	0.81[CEU][hapmap]
rs17129041	0.81[CEU][hapmap]
rs1925342	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs2312153	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795531	0.90[EUR][1000 genomes]
rs6588209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6588214	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6686606	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap]
rs6699123	0.81[CEU][hapmap]
rs6701907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6701988	0.92[EUR][1000 genomes]
rs72918447	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512692	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519639	0.88[EUR][1000 genomes]
rs7525509	0.87[JPT][hapmap]
rs7526812	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7535076	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7537440	0.86[JPT][hapmap]
rs7547794	0.87[JPT][hapmap]
rs7547857	0.87[JPT][hapmap]
rs7551301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963140	0.85[JPT][hapmap]

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	nsv1221	chr1:67047908-67092696	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11208930	SGIP1	cis	Whole Blood	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67058000-67092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:67084200-67099800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:67087600-67090400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:67088400-67091000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:67088800-67091200	Enhancers	NHDF-Ad	bronchial
8	chr1:67089200-67091200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:67089200-67091200	Enhancers	Osteobl	bone
10	chr1:67089200-67091600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:67089400-67090400	Enhancers	Fetal Heart	heart
12	chr1:67089400-67090800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:67089400-67090800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:67089400-67090800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:67089400-67090800	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:67089400-67090800	Enhancers	HSMMtube	muscle
17	chr1:67089400-67091000	Enhancers	Brain Hippocampus Middle	brain
18	chr1:67089400-67091200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:67089400-67091200	Enhancers	Brain Substantia Nigra	brain
20	chr1:67089400-67091200	Enhancers	NHLF	lung
21	chr1:67089400-67091400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:67089400-67092000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:67089600-67090600	Enhancers	HSMM	muscle
24	chr1:67089600-67090800	Enhancers	Brain Anterior Caudate	brain
25	chr1:67089600-67090800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:67089600-67090800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr1:67089600-67091200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:67089600-67091200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:67089600-67091200	Enhancers	Brain Angular Gyrus	brain
30	chr1:67089600-67091200	Enhancers	HMEC	breast
31	chr1:67089600-67092200	Weak transcription	Aorta	Aorta
32	chr1:67089800-67091600	Enhancers	NHEK	skin
33	chr1:67089800-67092600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:67090000-67090400	Flanking Active TSS	HUVEC	blood vessel
35	chr1:67090000-67091200	Enhancers	NH-A	brain

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