Variant report

Variant	rs3109112
Chromosome Location	chr7:112095622-112095623
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
2	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction
ENSG00000181016	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2074796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708609	0.84[ASN][1000 genomes]
rs2708610	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2708611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095025	0.89[ASN][1000 genomes]
rs3128386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3128388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3183621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4386904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1801262	chr7:112071795-112104179	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3109112	IFRD1	Cis_1M	lymphoblastoid	RTeQTL
rs3109112	LSMEM1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112095800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:112092600-112095800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr7:112092600-112095800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:112092600-112095800	Weak transcription	Placenta	Placenta
5	chr7:112092600-112098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:112092600-112099000	Weak transcription	Spleen	Spleen
7	chr7:112092600-112099800	Weak transcription	Esophagus	oesophagus
8	chr7:112092600-112099800	Weak transcription	Gastric	stomach
9	chr7:112092600-112102400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:112092600-112109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:112092800-112095800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:112092800-112097000	Weak transcription	Colonic Mucosa	Colon
14	chr7:112093000-112095800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:112093000-112095800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:112093000-112095800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:112093000-112095800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:112093000-112095800	Weak transcription	Fetal Kidney	kidney
19	chr7:112093000-112095800	Weak transcription	Fetal Thymus	thymus
20	chr7:112093000-112095800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:112093000-112098800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:112093000-112099800	Weak transcription	Thymus	Thymus
23	chr7:112093000-112109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:112093200-112095800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:112093200-112096000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:112093200-112097200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:112093400-112096400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:112093400-112096800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:112093600-112095800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:112093600-112095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:112093600-112095800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:112093600-112096200	Weak transcription	Brain Germinal Matrix	brain
33	chr7:112093800-112095800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:112093800-112096000	Weak transcription	Primary B cells from cord blood	blood
35	chr7:112093800-112096000	Enhancers	Duodenum Mucosa	Duodenum
36	chr7:112093800-112097000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:112093800-112097000	Weak transcription	Fetal Brain Female	brain
38	chr7:112093800-112098600	Weak transcription	Primary T cells from cord blood	blood
39	chr7:112094000-112095800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:112094000-112095800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:112094000-112095800	Weak transcription	Hela-S3	cervix
42	chr7:112094000-112096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:112094000-112096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:112094000-112096000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:112094000-112102200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:112094200-112095800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:112094200-112095800	Weak transcription	Fetal Lung	lung
50	chr7:112094200-112095800	Weak transcription	HSMMtube	muscle

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