Variant report

Variant	rs10916129
Chromosome Location	chr1:227557589-227557590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227503449..227507598-chr1:227555312..227559428,5	K562	blood:
2	chr1:227503449..227507598-chr1:227555312..227559110,4	K562	blood:
3	chr1:227506214..227507997-chr1:227555860..227558711,2	MCF-7	breast:
4	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
5	chr1:227544961..227546777-chr1:227556862..227559703,3	K562	blood:
6	chr1:227556870..227561275-chr1:227563192..227568675,6	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10458380	0.86[ASN][1000 genomes]
rs10753434	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799412	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916123	0.85[ASN][1000 genomes]
rs10916124	0.85[ASN][1000 genomes]
rs10916127	0.86[ASN][1000 genomes]
rs10916128	0.88[ASN][1000 genomes]
rs10916133	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12022275	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12023427	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12028523	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12047964	0.90[ASN][1000 genomes]
rs12057466	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12062358	0.92[ASN][1000 genomes]
rs12081061	0.85[ASN][1000 genomes]
rs16847682	0.91[ASN][1000 genomes]
rs16847690	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28654860	0.82[ASN][1000 genomes]
rs3014272	0.92[CEU][hapmap]
rs3014274	0.92[CEU][hapmap]
rs4075196	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4075861	0.91[ASN][1000 genomes]
rs4233226	0.91[JPT][hapmap]
rs4233227	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4294380	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4491034	0.92[CEU][hapmap]
rs4531260	0.92[ASN][1000 genomes]
rs4653497	0.91[ASN][1000 genomes]
rs4653498	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4653826	0.91[JPT][hapmap]
rs4653828	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4653831	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59718661	0.86[ASN][1000 genomes]
rs61833060	0.91[ASN][1000 genomes]
rs6690898	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs67343057	0.85[ASN][1000 genomes]
rs7519870	0.90[ASN][1000 genomes]
rs7541775	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7553358	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7555764	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556096	0.85[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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227556600-227559200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:227556800-227557600	Flanking Active TSS	K562	blood
4	chr1:227556800-227557800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:227556800-227558400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:227556800-227559000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:227556800-227560800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr1:227556800-227560800	Enhancers	Stomach Mucosa	stomach
9	chr1:227556800-227561200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:227556800-227561200	Enhancers	HUVEC	blood vessel
11	chr1:227557000-227558600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr1:227557000-227558600	Enhancers	HSMM	muscle
13	chr1:227557000-227558800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:227557000-227559000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:227557200-227558000	Weak transcription	HSMMtube	muscle
16	chr1:227557200-227558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:227557200-227558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:227557200-227559600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:227557200-227565400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:227557400-227558000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:227557400-227558400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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