Variant report

Variant	rs3738680
Chromosome Location	chr1:228261291-228261292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228191745..228192555-chr1:228261259..228261971,3	MCF-7	breast:
2	chr1:228257466..228261450-chr1:228360954..228363878,3	K562	blood:
3	chr1:228193335..228195504-chr1:228260630..228262645,2	MCF-7	breast:
4	chr1:228256397..228258359-chr1:228260087..228261703,2	MCF-7	breast:
5	chr1:228248925..228252171-chr1:228258918..228261969,3	MCF-7	breast:
6	chr1:228230109..228232010-chr1:228259554..228261382,2	MCF-7	breast:
7	chr1:228191736..228192588-chr1:228261257..228262099,3	K562	blood:
8	chr1:228191984..228194843-chr1:228260469..228263373,2	MCF-7	breast:
9	chr1:228190941..228192847-chr1:228260763..228262214,8	MCF-7	breast:
10	chr1:228230050..228232873-chr1:228260583..228263014,2	MCF-7	breast:
11	chr1:228259486..228261831-chr1:228263458..228267215,4	MCF-7	breast:
12	chr1:228186931..228189875-chr1:228260382..228263090,3	MCF-7	breast:
13	chr1:228187251..228191319-chr1:228259829..228263819,5	MCF-7	breast:
14	chr1:228196561..228199539-chr1:228260175..228262293,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1034792	0.86[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1048503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495278	1.00[ASW][hapmap]
rs10916262	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11577976	1.00[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.84[LWK][hapmap]
rs11582265	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11584499	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589513	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1188975	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs1188977	1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12033088	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12048010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1620734	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1745422	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070960	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295995	0.86[EUR][1000 genomes]
rs3738681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768329	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3795774	0.82[CHB][hapmap]
rs3820624	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41270175	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41270177	0.84[EUR][1000 genomes]
rs4653533	0.86[JPT][hapmap]
rs4653897	0.84[EUR][1000 genomes]
rs57146523	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57657087	0.81[EUR][1000 genomes]
rs61825130	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61825131	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61825133	0.97[ASN][1000 genomes]
rs61825135	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61825156	0.84[ASN][1000 genomes]
rs708126	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs72756204	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756209	0.81[AMR][1000 genomes]
rs7539664	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs822727	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs860301	1.00[EUR][1000 genomes]
rs882451	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9287011	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
12	nsv549281	chr1:228255433-228261291	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv549284	chr1:228255729-228261291	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3340317	chr1:228256629-228261427	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3738680	MIXL1	cis	cerebellum	SCAN
rs3738680	OBSCN	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228248200-228269000	Weak transcription	Right Atrium	heart
2	chr1:228258600-228269000	Weak transcription	Esophagus	oesophagus
3	chr1:228259600-228262000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228260200-228261800	Weak transcription	Spleen	Spleen
5	chr1:228260200-228268000	Weak transcription	Gastric	stomach
6	chr1:228260200-228269000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:228260800-228262000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:228260800-228262200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:228260800-228262200	Enhancers	Brain Germinal Matrix	brain
10	chr1:228261000-228261800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:228261000-228262200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:228261000-228262200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:228261000-228262200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:228261000-228262400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:228261000-228263200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:228261000-228263400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:228261200-228261600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
18	chr1:228261200-228262200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:228261200-228262200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:228261200-228262200	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr1:228261200-228263000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:228261200-228267600	Weak transcription	Ovary	ovary

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