Variant report

Variant	rs6660167
Chromosome Location	chr1:94888021-94888022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94883408..94885801-chr1:94885846..94888306,2	K562	blood:
2	chr1:94882805..94885755-chr1:94886317..94890931,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117528	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1023058	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165143	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165150	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12080254	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094329	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12142995	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404710	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12750904	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415758	0.84[ASN][1000 genomes]
rs4148045	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4148046	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148051	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4424519	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579764	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656819	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724829	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528491	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871097	chr1:94850443-94941890	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6660167	GCLM	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94884800-94889200	Weak transcription	Spleen	Spleen
2	chr1:94885000-94889800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:94885200-94889800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr1:94885200-94891000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:94885200-94907200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:94885200-94915000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:94885400-94889800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:94885600-94888600	Enhancers	Primary T cells from cord blood	blood
9	chr1:94885600-94889000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:94885600-94889200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:94885600-94889800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:94885600-94891200	Weak transcription	Adipose Nuclei	Adipose
13	chr1:94885600-94891800	Weak transcription	Fetal Stomach	stomach
14	chr1:94885800-94889000	Weak transcription	Brain Anterior Caudate	brain
15	chr1:94885800-94889400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:94885800-94889600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:94885800-94891000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:94885800-94891000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:94885800-94891400	Weak transcription	Fetal Lung	lung
20	chr1:94885800-94894000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:94885800-94894000	Weak transcription	Colonic Mucosa	Colon
22	chr1:94886000-94889200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:94886000-94889200	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:94886000-94889400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:94886000-94889400	Enhancers	Fetal Heart	heart
26	chr1:94886000-94889800	Enhancers	Stomach Mucosa	stomach
27	chr1:94886000-94891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:94886000-94891400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr1:94886000-94891400	Weak transcription	Fetal Kidney	kidney
30	chr1:94886000-94891600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:94886200-94888200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:94886200-94891400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:94886200-94891400	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:94886400-94888200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:94886400-94888800	Enhancers	Dnd41	blood
36	chr1:94886400-94889600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:94886400-94891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:94886600-94889400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:94886600-94889800	Enhancers	A549	lung
40	chr1:94886800-94891000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:94887000-94888200	Flanking Active TSS	Liver	Liver
42	chr1:94887000-94888200	Enhancers	Fetal Brain Male	brain
43	chr1:94887000-94888600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:94887000-94888800	Flanking Active TSS	HepG2	liver
45	chr1:94887000-94889600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:94887200-94888200	Flanking Active TSS	Fetal Thymus	thymus
47	chr1:94887200-94888200	Flanking Active TSS	Thymus	Thymus
48	chr1:94887200-94888400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:94887200-94889200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:94887200-94889600	Enhancers	Sigmoid Colon	Sigmoid Colon

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