Variant report

Variant	rs4653828
Chromosome Location	chr1:227518267-227518268
allele	A/G
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	chr1:227502332..227510114-chr1:227516981..227526964,21	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10753434	0.80[ASN][1000 genomes]
rs10799412	0.80[ASN][1000 genomes]
rs10916123	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916127	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916128	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916129	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10916133	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11484717	0.85[ASN][1000 genomes]
rs12022275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023427	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12028523	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035190	0.90[ASW][hapmap]
rs12047964	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12057466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062358	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12081061	0.81[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12085773	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16847682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847690	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28654860	0.85[ASN][1000 genomes]
rs4075196	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4075861	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233226	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]
rs4233227	0.82[CHB][hapmap]
rs4294380	0.80[CHB][hapmap]
rs4531260	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653497	0.93[ASN][1000 genomes]
rs4653498	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs4653826	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]
rs4653831	0.85[ASN][1000 genomes]
rs59718661	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61833060	0.93[ASN][1000 genomes]
rs6690898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67343057	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72632826	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72759365	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7519870	0.94[ASN][1000 genomes]
rs7540726	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7540833	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553358	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555764	0.81[ASN][1000 genomes]
rs7556096	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4653828	PGAM2	trans	parietal	SCAN
rs4653828	ARF1	cis	cerebellum	SCAN
rs4653828	CNIH4	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227512000-227523200	Weak transcription	Stomach Mucosa	stomach
2	chr1:227516800-227521800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:227517000-227518400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:227517400-227518400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:227518000-227518400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr1:227518000-227518400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:227518000-227518400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:227518000-227518600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:227518000-227518600	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:227518000-227518600	Enhancers	K562	blood
11	chr1:227518000-227519000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:227518000-227519000	Enhancers	Brain Hippocampus Middle	brain
13	chr1:227518200-227518400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:227518200-227518400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:227518200-227518400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:227518200-227518600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:227518200-227518600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:227518200-227518600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:227518200-227518600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:227518200-227518600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr1:227518200-227518600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:227518200-227518600	Enhancers	Brain Substantia Nigra	brain
23	chr1:227518200-227519000	Enhancers	Fetal Stomach	stomach

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