Variant report

Variant	rs11164962
Chromosome Location	chr1:94145933-94145934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94144888..94147261-chr1:94311172..94313468,2	K562	blood:
2	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12079723	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084853	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12092517	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1567791	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781002	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541387	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6656270	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657709	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6660740	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701871	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6702036	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704479	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7519952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs955470	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9659100	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94139200-94146000	Weak transcription	Liver	Liver
2	chr1:94140200-94146200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:94141000-94146200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:94141200-94146000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:94141400-94146200	Weak transcription	Aorta	Aorta
6	chr1:94142400-94146000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:94142400-94146000	Weak transcription	Pancreas	Pancrea
8	chr1:94143000-94146000	Weak transcription	Spleen	Spleen
9	chr1:94143400-94146000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:94143800-94146200	Transcr. at gene 5' and 3'	HMEC	breast
11	chr1:94143800-94146600	Transcr. at gene 5' and 3'	NHEK	skin
12	chr1:94144000-94146000	Enhancers	Fetal Intestine Small	intestine
13	chr1:94144400-94146400	Flanking Active TSS	HUVEC	blood vessel
14	chr1:94144400-94148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:94144600-94146000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:94144600-94146000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr1:94144600-94146200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:94144600-94148400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:94144800-94146000	Enhancers	Fetal Lung	lung
20	chr1:94144800-94146200	Weak transcription	Small Intestine	intestine
21	chr1:94144800-94146400	Flanking Active TSS	NHLF	lung
22	chr1:94144800-94146400	Flanking Active TSS	Osteobl	bone
23	chr1:94145000-94146000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:94145000-94146400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:94145000-94146600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:94145000-94148000	Active TSS	Brain Anterior Caudate	brain
27	chr1:94145200-94146000	Enhancers	Colon Smooth Muscle	Colon
28	chr1:94145200-94146400	Flanking Active TSS	HSMMtube	muscle
29	chr1:94145200-94148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:94145400-94146000	Enhancers	Primary B cells from peripheral blood	blood
31	chr1:94145400-94146000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:94145400-94146000	Active TSS	Brain Cingulate Gyrus	brain
33	chr1:94145400-94147600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:94145400-94147800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:94145400-94148400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:94145400-94148400	Active TSS	HSMM	muscle
37	chr1:94145600-94146000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:94145600-94146000	Active TSS	NH-A	brain
39	chr1:94145600-94146200	Enhancers	Stomach Mucosa	stomach
40	chr1:94145600-94146400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:94145600-94146400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:94145600-94147600	Active TSS	Fetal Kidney	kidney
43	chr1:94145600-94147800	Active TSS	NHDF-Ad	bronchial
44	chr1:94145600-94148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:94145600-94148200	Active TSS	A549	lung
46	chr1:94145800-94146000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:94145800-94146000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:94145800-94146000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:94145800-94146000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr1:94145800-94146000	Enhancers	Colonic Mucosa	Colon

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