Variant report

Variant	rs6898275
Chromosome Location	chr5:178138449-178138450
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	chr5:178130386..178132471-chr5:178136423..178139272,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1000057	0.88[ASN][1000 genomes]
rs10042073	0.88[ASN][1000 genomes]
rs10072060	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12518753	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13188788	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1984703	0.88[ASN][1000 genomes]
rs2078257	0.88[ASN][1000 genomes]
rs3927097	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246821	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7704813	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7711731	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7715476	0.88[ASN][1000 genomes]
rs7736628	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs931056	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6898275	ZNF354B	cis	cerebellum	SCAN
rs6898275	PDLIM7	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178130000-178150600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr5:178135400-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178135800-178147600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
4	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
5	chr5:178136200-178155200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr5:178136400-178138600	Weak transcription	Fetal Heart	heart
7	chr5:178136600-178141000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
8	chr5:178136800-178150400	ZNF genes & repeats	Brain Substantia Nigra	brain
9	chr5:178136800-178150600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:178136800-178152800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr5:178137000-178149800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr5:178137000-178150600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:178137000-178150600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
14	chr5:178137200-178151000	ZNF genes & repeats	Fetal Brain Female	brain
15	chr5:178137400-178139800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:178137400-178147800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:178137400-178150600	ZNF genes & repeats	Psoas Muscle	Psoas
18	chr5:178137800-178139400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:178138000-178138800	Weak transcription	Fetal Kidney	kidney
20	chr5:178138000-178139400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:178138000-178139800	Strong transcription	Brain Germinal Matrix	brain
22	chr5:178138200-178140600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:178138400-178139800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:178138400-178141800	Strong transcription	Placenta	Placenta
25	chr5:178138400-178146000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
26	chr5:178138400-178149800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:178138400-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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