Variant report

Variant	rs17589349
Chromosome Location	chr4:151464906-151464907
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151454348..151457319-chr4:151460671..151464936,3	K562	blood:
2	chr4:151464421..151466490-chr4:151508442..151510981,2	K562	blood:
3	chr4:151464361..151466235-chr4:151513578..151516173,2	K562	blood:
4	chr4:151454348..151457319-chr4:151462077..151464936,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12498862	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500337	0.84[ASN][1000 genomes]
rs12503093	0.84[ASN][1000 genomes]
rs12506612	0.91[ASN][1000 genomes]
rs12507785	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12508149	0.84[ASN][1000 genomes]
rs12647325	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589028	0.84[ASN][1000 genomes]
rs17589134	0.84[ASN][1000 genomes]
rs1979920	0.84[ASN][1000 genomes]
rs2036552	0.84[ASN][1000 genomes]
rs2360071	0.84[ASN][1000 genomes]
rs6812262	0.84[ASN][1000 genomes]
rs6817796	0.84[ASN][1000 genomes]
rs6827645	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831707	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836012	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839345	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6854612	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6855729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7677055	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs8180280	0.90[CHB][hapmap]
rs952097	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs998069	0.94[AMR][1000 genomes];0.98[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	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1018942	chr4:151423295-151556444	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv537301	chr4:151423295-151556444	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17589349	PLRG1	cis	parietal	SCAN
rs17589349	LRBA	cis	parietal	SCAN
rs17589349	TTC29	cis	cerebellum	SCAN
rs17589349	LRBA	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151422800-151474600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:151440200-151472600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:151445000-151472600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:151453200-151474600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:151455200-151473200	Weak transcription	Fetal Intestine Small	intestine
6	chr4:151460000-151465400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:151460000-151474600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:151462200-151474600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:151462400-151467000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:151462400-151467200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:151462400-151467800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:151462600-151467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:151462600-151467000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:151462600-151467200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:151462600-151467400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:151462600-151467800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:151463200-151467200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:151464600-151465600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:151464800-151466200	Enhancers	K562	blood
20	chr4:151464800-151468600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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