Variant report

Variant	rs4446934
Chromosome Location	chr1:224381403-224381404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224372056..224374246-chr1:224379708..224382000,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10495222	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs1060386	0.95[ASN][1000 genomes]
rs10799529	0.89[ASN][1000 genomes]
rs10799551	0.86[CHB][hapmap]
rs10916468	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10916489	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10916515	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs10916543	0.81[CHB][hapmap]
rs11588603	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11588981	0.95[ASN][1000 genomes]
rs12024159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134258	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs12135557	0.94[CHB][hapmap]
rs12142842	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143450	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12143576	0.95[ASN][1000 genomes]
rs1533589	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2405302	0.84[ASN][1000 genomes]
rs4290029	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4653997	0.83[ASN][1000 genomes]
rs4654009	0.86[CHB][hapmap];0.84[MEX][hapmap]
rs4654010	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs55977521	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023673	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426060	0.91[ASN][1000 genomes]
rs6664230	0.86[CHB][hapmap]
rs6668744	0.82[ASN][1000 genomes]
rs6674695	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6682662	0.88[ASN][1000 genomes]
rs72753995	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72755906	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72755909	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72755914	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72755915	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72755917	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7541131	0.82[ASN][1000 genomes]
rs908802	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908804	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4446934	DEGS1	cis	multi-tissue	Pritchard
rs4446934	FBXO28	cis	lymphoblastoid	seeQTL
rs4446934	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
2	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224372600-224392400	Weak transcription	Ovary	ovary
4	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:224373200-224382000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
9	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine
10	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
11	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
14	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:224373800-224384200	Weak transcription	Fetal Brain Male	brain
16	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
17	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
18	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:224374000-224384800	Weak transcription	Stomach Mucosa	stomach
20	chr1:224374000-224391000	Weak transcription	Spleen	Spleen
21	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
22	chr1:224374200-224382000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:224375000-224383000	Weak transcription	Gastric	stomach
24	chr1:224375200-224382200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:224376000-224382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:224376400-224383000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:224376800-224382000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:224377200-224382400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:224377200-224382600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:224377200-224382600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:224377200-224383200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:224377200-224383200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:224377200-224384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:224377400-224381600	Strong transcription	Fetal Intestine Large	intestine
35	chr1:224377400-224382000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:224377400-224382000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:224377400-224382000	Strong transcription	Adipose Nuclei	Adipose
38	chr1:224377400-224382000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:224377400-224382200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:224377400-224382200	Strong transcription	Placenta	Placenta
41	chr1:224377400-224382200	Strong transcription	Fetal Thymus	thymus
42	chr1:224377400-224382400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:224377400-224382400	Strong transcription	Dnd41	blood
44	chr1:224377400-224382600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:224377400-224383200	Strong transcription	Primary T cells from cord blood	blood
46	chr1:224377400-224383200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:224377400-224383200	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:224377400-224383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:224377400-224383600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:224377400-224383600	Strong transcription	Fetal Stomach	stomach

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