Variant report

Variant	rs2953638
Chromosome Location	chr1:227520592-227520593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227514733..227517103-chr1:227519099..227520734,2	K562	blood:
2	chr1:227505215..227507825-chr1:227516537..227520838,4	MCF-7	breast:
3	chr1:227519023..227520761-chr1:227558780..227560825,2	MCF-7	breast:
4	chr1:227510287..227513038-chr1:227518818..227521633,2	MCF-7	breast:
5	chr1:227505014..227506615-chr1:227519753..227521661,2	MCF-7	breast:
6	chr1:227502332..227510114-chr1:227516981..227526964,21	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10495255	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12035986	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12044287	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs12137591	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs12565871	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs2953637	0.83[ASN][1000 genomes]
rs2953641	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953643	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953645	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953650	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2953652	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2953653	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2953655	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2953656	0.93[ASN][1000 genomes]
rs3014252	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3014253	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs3014256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014263	0.99[ASN][1000 genomes]
rs3014267	0.89[JPT][hapmap]
rs3014271	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3795457	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs4339829	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs6700730	0.82[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
rs2953638	DNAH14	cis	parietal	SCAN
rs2953638	PRSS38	cis	parietal	SCAN
rs2953638	PARP1	cis	cerebellum	SCAN

Chromatin state (count:4 , 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	chr1:227518600-227521200	Weak transcription	K562	blood
4	chr1:227520400-227520800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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