Variant report

Variant	rs2953645
Chromosome Location	chr1:227532129-227532130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227530329..227533212-chr1:227543637..227546131,2	K562	blood:
2	chr1:227531951..227533519-chr1:227535899..227538249,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10495255	0.94[JPT][hapmap]
rs12035986	1.00[JPT][hapmap]
rs12044287	0.94[JPT][hapmap]
rs12137591	0.94[JPT][hapmap]
rs12565871	0.94[JPT][hapmap]
rs2953637	0.84[ASN][1000 genomes]
rs2953638	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953641	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2953643	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953650	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953652	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953653	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2953655	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2953656	0.94[ASN][1000 genomes]
rs3014252	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3014253	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs3014256	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3014263	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014267	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs3014271	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795457	0.93[JPT][hapmap]
rs4339829	0.94[JPT][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2953645	PRSS38	cis	parietal	SCAN
rs2953645	PARP1	cis	cerebellum	SCAN
rs2953645	AIDA	cis	cerebellum	SCAN
rs2953645	CABC1	cis	cerebellum	SCAN
rs2953645	DNAH14	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227530400-227532600	Enhancers	HSMM	muscle
2	chr1:227530600-227532600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:227530800-227533000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:227531000-227532400	Enhancers	NHDF-Ad	bronchial
5	chr1:227531000-227532600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:227531000-227532600	Enhancers	Osteobl	bone
7	chr1:227531000-227532800	Enhancers	NHLF	lung
8	chr1:227531200-227532200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227531200-227532400	Enhancers	Fetal Lung	lung
10	chr1:227531200-227532600	Enhancers	Hela-S3	cervix
11	chr1:227531200-227532600	Enhancers	HMEC	breast
12	chr1:227531200-227532600	Enhancers	NHEK	skin
13	chr1:227531400-227532200	Weak transcription	HSMMtube	muscle
14	chr1:227531400-227532400	Enhancers	HUVEC	blood vessel
15	chr1:227531400-227532800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:227531600-227532200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:227531600-227532400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:227531600-227532400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:227531600-227532400	Enhancers	NH-A	brain
20	chr1:227531600-227532600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:227531800-227532200	Flanking Active TSS	A549	lung
22	chr1:227531800-227532400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:227531800-227532400	Enhancers	K562	blood
24	chr1:227532000-227532400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:227532000-227532400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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