Variant report

Variant	rs333993
Chromosome Location	chr2:179144028-179144029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179134962..179137702-chr2:179142428..179144943,2	K562	blood:
2	chr2:179058030..179060650-chr2:179143594..179145205,2	K562	blood:
3	chr2:179140566..179142281-chr2:179143545..179145094,2	K562	blood:
4	chr2:179125831..179128251-chr2:179141469..179144423,2	K562	blood:
5	chr2:179058860..179061144-chr2:179142377..179144117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs101266	0.94[JPT][hapmap]
rs12185670	0.81[JPT][hapmap]
rs12476671	0.93[JPT][hapmap]
rs1434080	0.83[JPT][hapmap]
rs147180	0.94[JPT][hapmap]
rs333992	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333994	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333997	0.94[JPT][hapmap]
rs334002	0.88[CEU][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs334009	0.93[JPT][hapmap]
rs334013	0.94[JPT][hapmap]
rs334014	0.94[JPT][hapmap]
rs334037	0.81[JPT][hapmap]
rs334604	0.85[CEU][hapmap]
rs334616	0.88[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs334620	0.82[JPT][hapmap]
rs334622	0.82[JPT][hapmap]
rs334623	0.89[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs334630	0.82[JPT][hapmap]
rs334631	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs551368	0.94[JPT][hapmap]
rs7587549	0.83[JPT][hapmap]
rs7592114	0.86[MEX][hapmap]
rs7599683	0.88[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs9989738	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs333993	LOC100130691	cis	cerebellum	SCAN
rs333993	FKBP7	cis	cerebellum	SCAN
rs333993	OLA1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179133800-179146800	Weak transcription	Esophagus	oesophagus
2	chr2:179136800-179146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:179141000-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:179141200-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:179141600-179145600	Enhancers	Fetal Intestine Small	intestine
6	chr2:179142000-179144600	Enhancers	HSMM	muscle
7	chr2:179142200-179144600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:179142200-179144600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:179142400-179144200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:179142400-179144200	Enhancers	NHEK	skin
11	chr2:179142400-179144400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:179142400-179144600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:179142400-179144600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:179142400-179144600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:179142400-179144800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:179142400-179145000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:179142400-179145000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:179142400-179145200	Enhancers	Fetal Intestine Large	intestine
19	chr2:179142400-179145200	Enhancers	NHDF-Ad	bronchial
20	chr2:179142600-179144200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:179142600-179144600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:179142600-179144600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:179142800-179144200	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:179142800-179144400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:179142800-179144400	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr2:179142800-179144800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:179142800-179145200	Enhancers	HUVEC	blood vessel
28	chr2:179142800-179146600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:179142800-179146800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:179142800-179146800	Weak transcription	Brain Angular Gyrus	brain
31	chr2:179143000-179144200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:179143000-179144600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:179143000-179144600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:179143000-179144600	Enhancers	Osteobl	bone
35	chr2:179143000-179145000	Enhancers	Liver	Liver
36	chr2:179143000-179145000	Enhancers	NH-A	brain
37	chr2:179143000-179146600	Weak transcription	A549	lung
38	chr2:179143000-179146800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:179143000-179146800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:179143000-179146800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:179143000-179160200	Weak transcription	Fetal Kidney	kidney
42	chr2:179143200-179144600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:179143200-179144600	Enhancers	K562	blood
44	chr2:179143200-179144800	Enhancers	HepG2	liver
45	chr2:179143200-179160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
47	chr2:179143400-179146800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:179143600-179144600	Enhancers	Hela-S3	cervix
49	chr2:179143600-179144800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:179143600-179145400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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