Variant report

Variant	rs6074639
Chromosome Location	chr20:13748615-13748616
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13745856..13749163-chr20:13765224..13767517,3	MCF-7	breast:
2	chr2:186715733..186716239-chr20:13748197..13748697,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101247	Chromatin interaction
ENSG00000089048	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2094652	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2423754	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs243917	1.00[EUR][1000 genomes]
rs34901599	1.00[AMR][1000 genomes]
rs4239710	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814259	0.85[AFR][1000 genomes]
rs6033822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042326	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042334	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6079175	0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109967	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats 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
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6074639	LOC728606	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
2	chr20:13734000-13763200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr20:13736800-13763800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:13740800-13757600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr20:13741800-13763200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr20:13741800-13763800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:13742000-13757600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr20:13742000-13757800	Strong transcription	NH-A	brain
9	chr20:13742000-13759000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr20:13742000-13762600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:13742200-13763600	Strong transcription	Liver	Liver
12	chr20:13742400-13749200	Strong transcription	HSMM	muscle
13	chr20:13742400-13763800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr20:13742800-13752400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr20:13743000-13750400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:13743000-13752200	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr20:13743800-13751400	Strong transcription	Placenta	Placenta
18	chr20:13743800-13752000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr20:13743800-13758000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr20:13743800-13758200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr20:13743800-13763600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr20:13744000-13749200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr20:13744000-13752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr20:13744000-13758200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr20:13744200-13752600	Strong transcription	Osteobl	bone
26	chr20:13744400-13752800	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr20:13744400-13758600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:13744400-13763200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr20:13744600-13749000	Strong transcription	Fetal Brain Male	brain
30	chr20:13744800-13751400	Strong transcription	Left Ventricle	heart
31	chr20:13744800-13753800	Strong transcription	Fetal Thymus	thymus
32	chr20:13745000-13749000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:13745000-13749000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr20:13745000-13749000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr20:13745000-13750200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:13745000-13750600	Strong transcription	Thymus	Thymus
37	chr20:13745000-13751600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:13745000-13751800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:13745000-13751800	Strong transcription	Ovary	ovary
40	chr20:13745000-13757600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:13745200-13750400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr20:13745200-13751600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr20:13745400-13749200	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr20:13745400-13751600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr20:13745400-13751800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr20:13745400-13751800	Strong transcription	Brain Substantia Nigra	brain
47	chr20:13745400-13752000	Strong transcription	Brain Angular Gyrus	brain
48	chr20:13745600-13748800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:13745600-13749000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr20:13745600-13750000	Weak transcription	K562	blood

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