Variant report

Variant	rs4233226
Chromosome Location	chr1:227518041-227518042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227505954..227508280-chr1:227516746..227520038,3	K562	blood:
2	chr1:227505215..227507825-chr1:227516537..227520838,4	MCF-7	breast:
3	chr1:227511205..227513066-chr1:227516243..227518388,2	MCF-7	breast:
4	chr1:227515846..227518082-chr1:227521897..227524697,2	MCF-7	breast:
5	chr1:227502332..227510114-chr1:227516981..227526964,21	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10916123	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10916124	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10916127	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10916128	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10916129	0.91[JPT][hapmap]
rs10916133	0.87[JPT][hapmap]
rs11484717	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12022275	0.81[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12023427	0.81[CEU][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12028523	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12047964	0.85[ASN][1000 genomes]
rs12057466	0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12062358	0.82[ASN][1000 genomes]
rs12081061	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12085773	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16847682	0.84[ASN][1000 genomes]
rs16847690	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs28654860	0.93[ASN][1000 genomes]
rs3014272	0.82[CHB][hapmap]
rs3014274	0.82[CHB][hapmap]
rs4075196	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4075861	0.84[ASN][1000 genomes]
rs4491034	0.82[CHB][hapmap]
rs4531260	0.82[ASN][1000 genomes]
rs4653497	0.84[ASN][1000 genomes]
rs4653498	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4653826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[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];1.00[ASN][1000 genomes]
rs4653828	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59718661	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61833060	0.84[ASN][1000 genomes]
rs6690898	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs67343057	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72632826	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72759365	0.84[AMR][1000 genomes]
rs7519870	0.85[ASN][1000 genomes]
rs7540726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540833	0.84[ASN][1000 genomes]
rs7541775	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7553358	0.81[CEU][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7556096	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4233226	CNIH4	cis	cerebellum	SCAN
rs4233226	CDC42BPA	cis	cerebellum	SCAN
rs4233226	CCDC67	trans	parietal	SCAN
rs4233226	ARF1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227512000-227523200	Weak transcription	Stomach Mucosa	stomach
3	chr1:227516600-227518200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:227516800-227518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:227516800-227518200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:227516800-227518200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:227516800-227521800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227517000-227518200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:227517000-227518400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:227517400-227518400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:227518000-227518400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr1:227518000-227518400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:227518000-227518400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227518000-227518600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:227518000-227518600	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:227518000-227518600	Enhancers	K562	blood
17	chr1:227518000-227519000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:227518000-227519000	Enhancers	Brain Hippocampus Middle	brain

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