Variant report

Variant	rs399649
Chromosome Location	chr1:94097441-94097442
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94096921..94097933-chr1:94146005..94146828,3	MCF-7	breast:
2	chr1:94096748..94098935-chr1:94106081..94108705,3	K562	blood:
3	chr1:94096488..94097857-chr1:94279258..94281095,8	MCF-7	breast:
4	chr1:94096882..94097807-chr1:94279318..94280136,2	MCF-7	breast:
5	chr1:94091548..94098915-chr1:94308687..94313875,7	K562	blood:
6	chr1:93965020..93966989-chr1:94096197..94098181,2	K562	blood:
7	chr1:94097057..94097800-chr1:94146342..94146876,2	MCF-7	breast:

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

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12084853	1.00[JPT][hapmap]
rs12568405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1618866	0.94[ASN][1000 genomes]
rs1740068	0.94[ASN][1000 genomes]
rs1772781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772782	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182913	0.91[ASN][1000 genomes]
rs183538	0.94[ASN][1000 genomes]
rs236266	1.00[JPT][hapmap]
rs236267	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236270	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236271	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236273	0.86[ASN][1000 genomes]
rs236274	0.91[ASN][1000 genomes]
rs236275	0.91[ASN][1000 genomes]
rs236277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236278	0.91[ASN][1000 genomes]
rs236281	0.91[ASN][1000 genomes]
rs236292	0.80[EUR][1000 genomes]
rs236295	1.00[JPT][hapmap]
rs236296	1.00[JPT][hapmap]
rs236306	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs236307	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs236308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs236311	0.83[ASN][1000 genomes]
rs236312	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs236313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236331	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs236343	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs236344	0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs368888	0.90[ASN][1000 genomes]
rs3767975	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3767979	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3767981	0.93[ASN][1000 genomes]
rs3767987	0.93[ASN][1000 genomes]
rs3767991	1.00[JPT][hapmap]
rs423493	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs60159857	0.94[ASN][1000 genomes]
rs6541387	1.00[JPT][hapmap]
rs6671749	0.83[EUR][1000 genomes]
rs6702036	1.00[JPT][hapmap]
rs6704479	1.00[JPT][hapmap]
rs7518795	0.83[EUR][1000 genomes]
rs7519939	0.83[EUR][1000 genomes]
rs7551964	0.83[EUR][1000 genomes]
rs798213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs798217	0.81[ASN][1000 genomes]
rs798218	0.84[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs399649	HSS00223805	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
4	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:94085400-94107600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:94086800-94098000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:94086800-94101200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:94088400-94100400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:94088600-94118800	Weak transcription	Gastric	stomach
11	chr1:94090400-94101400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:94090600-94101400	Weak transcription	Right Ventricle	heart
13	chr1:94091600-94101000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:94091600-94101400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:94091600-94106600	Weak transcription	Aorta	Aorta
16	chr1:94091600-94107600	Weak transcription	Ovary	ovary
17	chr1:94091800-94117400	Weak transcription	Fetal Lung	lung
18	chr1:94092200-94097800	Genic enhancers	HMEC	breast
19	chr1:94092200-94100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:94092200-94101000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:94093000-94100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:94093200-94100600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:94093600-94097800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:94093800-94097800	Genic enhancers	Muscle Satellite Cultured Cells	--
25	chr1:94093800-94098000	Genic enhancers	Hela-S3	cervix
26	chr1:94094000-94100400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:94094000-94100400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:94094000-94101200	Weak transcription	Left Ventricle	heart
29	chr1:94094200-94101200	Weak transcription	Lung	lung
30	chr1:94094200-94101200	Weak transcription	Right Atrium	heart
31	chr1:94094200-94120400	Weak transcription	Psoas Muscle	Psoas
32	chr1:94094600-94100400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:94095000-94100400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:94095000-94101600	Weak transcription	HSMMtube	muscle
35	chr1:94095400-94101200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:94095600-94098200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:94095600-94100400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:94095600-94100600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:94095600-94100600	Weak transcription	NHLF	lung
40	chr1:94095600-94101200	Weak transcription	HUVEC	blood vessel
41	chr1:94095600-94101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:94095600-94125400	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:94095800-94100400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:94096200-94098000	Strong transcription	NH-A	brain
45	chr1:94096200-94100600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:94096400-94097800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:94096600-94097800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:94096600-94097800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr1:94096600-94098000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:94096800-94098000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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