Variant report

Variant	rs2554399
Chromosome Location	chr8:95700688-95700689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DPY19L4-2	chr8:95700456-95700838	NONHSAT127791

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10089502	0.94[EUR][1000 genomes]
rs10109430	0.89[CHB][hapmap];0.93[MEX][hapmap]
rs10110480	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11782734	0.95[EUR][1000 genomes]
rs11786992	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13258807	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2554400	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2554401	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2722885	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2722886	0.94[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2890826	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4735314	0.93[EUR][1000 genomes]
rs6471480	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs67113852	0.95[EUR][1000 genomes]
rs67760346	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71532328	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7815731	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9297945	0.89[CHB][hapmap]

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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2554399	HRSP12	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95655600-95701200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:95656400-95701000	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr8:95656400-95713000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr8:95656600-95701200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:95656600-95701600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:95656600-95703200	Weak transcription	Stomach Mucosa	stomach
7	chr8:95657200-95701200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr8:95670800-95703000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:95680600-95718400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:95681400-95704400	Weak transcription	Gastric	stomach
11	chr8:95690200-95701000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr8:95690200-95701200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr8:95690600-95722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:95691000-95712200	Weak transcription	Colonic Mucosa	Colon
15	chr8:95691400-95706800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr8:95691800-95701800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:95692000-95701600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:95693600-95701200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr8:95695000-95712200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:95696800-95700800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:95697200-95704400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr8:95697200-95712200	Weak transcription	Esophagus	oesophagus
23	chr8:95698000-95704400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:95698600-95704400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:95698600-95704400	Weak transcription	Fetal Intestine Small	intestine
26	chr8:95698600-95714200	Weak transcription	Fetal Kidney	kidney
27	chr8:95699200-95701000	Strong transcription	Placenta	Placenta
28	chr8:95699200-95701200	Strong transcription	HMEC	breast
29	chr8:95699600-95700800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr8:95700000-95701000	Strong transcription	NHEK	skin
31	chr8:95700200-95701000	Strong transcription	Fetal Intestine Large	intestine
32	chr8:95700200-95701000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr8:95700400-95700800	Strong transcription	Pancreas	Pancrea
34	chr8:95700400-95701000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr8:95700400-95701400	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr8:95700400-95719800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr8:95700600-95700800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
38	chr8:95700600-95701000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr8:95700600-95701200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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