Variant report

Variant	rs849904
Chromosome Location	chr1:228137145-228137146
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:228137060-228137210	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:
2	chr1:227962379..227965351-chr1:228135797..228137632,2	MCF-7	breast:
3	chr1:228136513..228138396-chr1:228142970..228145012,2	K562	blood:

Variant related genes	Relation type
WNT9A	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10916245	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636192	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1774755	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2313118	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527614	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527615	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2527616	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2796056	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094912	0.85[CEU][hapmap]
rs3094915	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653889	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590657	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591582	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594916	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596208	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs596675	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs605410	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621372	0.81[EUR][1000 genomes]
rs621631	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621963	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs631768	0.95[AFR][1000 genomes]
rs632832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634106	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs635563	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs638877	0.84[AFR][1000 genomes]
rs644794	0.81[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658238	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs672907	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs672977	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs673726	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs686533	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs708112	0.83[CEU][hapmap]
rs708114	0.80[CEU][hapmap]
rs849903	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	esv3344015	chr1:228134354-228137302	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs849904	OBSCN	cis	Esophagus Mucosa	GTEx
rs849904	C1orf145	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228136200-228137200	Flanking Active TSS	Fetal Lung	lung
2	chr1:228136200-228137200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
3	chr1:228136200-228137200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:228136200-228137200	Flanking Active TSS	HSMM	muscle
5	chr1:228136600-228137200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:228136600-228137200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:228136600-228137200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:228136600-228137200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:228136600-228137400	Bivalent Enhancer	Fetal Intestine Large	intestine
10	chr1:228136600-228137400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:228136600-228137800	Enhancers	Fetal Brain Male	brain
12	chr1:228136800-228137200	Enhancers	Colon Smooth Muscle	Colon
13	chr1:228136800-228137200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr1:228136800-228137200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
15	chr1:228136800-228137200	Bivalent Enhancer	Right Ventricle	heart
16	chr1:228136800-228137400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:228136800-228137400	Bivalent Enhancer	Brain Germinal Matrix	brain
18	chr1:228136800-228138000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr1:228136800-228138000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:228136800-228139600	Weak transcription	Esophagus	oesophagus
21	chr1:228136800-228141000	Weak transcription	Ovary	ovary
22	chr1:228136800-228141000	Weak transcription	NHDF-Ad	bronchial
23	chr1:228137000-228137200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:228137000-228137200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
25	chr1:228137000-228137200	Flanking Active TSS	Fetal Brain Female	brain
26	chr1:228137000-228137600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:228137000-228137600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:228137000-228137600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:228137000-228137800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:228137000-228141000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links