Variant report

Variant	rs2490026
Chromosome Location	chr6:38670067-38670068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38656830..38658689-chr6:38669303..38670813,2	MCF-7	breast:
2	chr6:38606456..38608908-chr6:38667468..38670067,2	MCF-7	breast:
3	chr6:38654394..38655965-chr6:38667989..38670845,2	MCF-7	breast:
4	chr6:38668625..38670754-chr9:86321990..86324896,2	K562	blood:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1049346	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs1621788	0.92[CEU][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap]
rs1781717	0.88[EUR][1000 genomes]
rs1781719	0.88[EUR][1000 genomes]
rs1781732	0.80[AFR][1000 genomes]
rs1781734	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs1781735	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2490026	GLO1	cis	parietal	SCAN
rs2490026	GLO1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38663600-38670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:38668400-38670200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:38669000-38671400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:38669200-38671000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:38669200-38671400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:38669400-38670200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:38669400-38671000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:38669400-38671000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:38669400-38671000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:38669400-38671000	Active TSS	Primary T cells from cord blood	blood
11	chr6:38669400-38671200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:38669400-38671200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:38669400-38671400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:38669400-38671400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:38669400-38671400	Active TSS	NHLF	lung
16	chr6:38669600-38670400	Flanking Active TSS	Dnd41	blood
17	chr6:38669600-38671000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:38669600-38671000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:38669600-38671000	Active TSS	HMEC	breast
20	chr6:38669600-38671000	Active TSS	HUVEC	blood vessel
21	chr6:38669600-38671000	Active TSS	NHEK	skin
22	chr6:38669600-38671200	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:38669600-38671200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:38669600-38671200	Active TSS	K562	blood
25	chr6:38669600-38671400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:38669600-38671400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:38669800-38670200	Flanking Active TSS	HepG2	liver
28	chr6:38669800-38670400	Flanking Active TSS	Osteobl	bone
29	chr6:38669800-38670600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:38669800-38671000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:38669800-38671000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:38669800-38671000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:38669800-38671000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:38669800-38671000	Active TSS	Lung	lung
35	chr6:38669800-38671000	Active TSS	Rectal Smooth Muscle	rectum
36	chr6:38669800-38671000	Active TSS	HSMM	muscle
37	chr6:38669800-38671200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:38669800-38671200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:38669800-38671200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:38669800-38671200	Active TSS	Duodenum Mucosa	Duodenum
41	chr6:38669800-38671200	Active TSS	GM12878-XiMat	blood
42	chr6:38669800-38671400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:38669800-38671400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:38669800-38671400	Active TSS	Stomach Smooth Muscle	stomach
45	chr6:38669800-38671400	Active TSS	NH-A	brain
46	chr6:38669800-38671600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:38669800-38671600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:38670000-38670200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:38670000-38670200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:38670000-38670200	Enhancers	Primary neutrophils fromperipheralblood	blood

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