Variant report

Variant	rs17622621
Chromosome Location	chr6:38669184-38669185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38606456..38608908-chr6:38667468..38670067,2	MCF-7	breast:
2	chr6:38654394..38655965-chr6:38667989..38670845,2	MCF-7	breast:
3	chr6:38668625..38670754-chr9:86321990..86324896,2	K562	blood:
4	chr6:38626742..38628981-chr6:38666689..38669446,2	K562	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12198313	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12202097	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12206647	0.92[CEU][hapmap]
rs12209475	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12209477	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210866	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194237	0.82[JPT][hapmap]
rs13200763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203767	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1937778	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1937780	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36138100	0.86[AMR][1000 genomes]
rs71571343	0.92[AMR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17622621	GLO1	cis	parietal	SCAN
rs17622621	MDFI	cis	cerebellum	SCAN
rs17622621	ANKS1A	cis	cerebellum	SCAN
rs17622621	GLO1	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:38646000-38670000	Weak transcription	A549	lung
4	chr6:38648800-38669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:38651200-38669800	Weak transcription	HSMM	muscle
6	chr6:38651200-38670000	Weak transcription	Fetal Kidney	kidney
7	chr6:38651400-38669400	Weak transcription	Osteobl	bone
8	chr6:38653000-38670000	Weak transcription	NHDF-Ad	bronchial
9	chr6:38653600-38669400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:38654400-38669800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:38654600-38669400	Weak transcription	Hela-S3	cervix
12	chr6:38655200-38669800	Weak transcription	Pancreas	Pancrea
13	chr6:38655200-38670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:38657000-38669400	Weak transcription	Thymus	Thymus
15	chr6:38657000-38669800	Weak transcription	Colonic Mucosa	Colon
16	chr6:38657000-38669800	Weak transcription	Lung	lung
17	chr6:38657000-38670000	Weak transcription	Left Ventricle	heart
18	chr6:38657000-38670000	Weak transcription	Psoas Muscle	Psoas
19	chr6:38657600-38669600	Weak transcription	Fetal Brain Male	brain
20	chr6:38663600-38670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:38665200-38669800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr6:38665200-38670000	Weak transcription	Right Atrium	heart
23	chr6:38665400-38669400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:38665600-38669600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr6:38666000-38669400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:38666600-38669600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:38666600-38669800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:38666600-38670000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:38666800-38669400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:38666800-38670000	Weak transcription	Brain Angular Gyrus	brain
31	chr6:38667000-38670000	Weak transcription	Small Intestine	intestine
32	chr6:38667400-38669200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:38667400-38670000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:38667800-38669200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr6:38667800-38669600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:38668000-38669200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:38668000-38669200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:38668000-38669600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
39	chr6:38668000-38669600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr6:38668000-38669600	ZNF genes & repeats	GM12878-XiMat	blood
41	chr6:38668000-38669600	ZNF genes & repeats	K562	blood
42	chr6:38668000-38669800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:38668200-38669200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:38668200-38669400	Strong transcription	HMEC	breast
45	chr6:38668200-38669800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:38668400-38669200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:38668400-38669200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:38668400-38669200	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:38668400-38669400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:38668400-38669400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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