Variant report

Variant	rs957184
Chromosome Location	chr13:39915646-39915647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12856032	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1333439	0.85[EUR][1000 genomes]
rs1924315	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2147127	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2324258	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2985186	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4340188	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6563698	0.89[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs7318557	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321424	0.85[EUR][1000 genomes]
rs7335060	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7338314	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs747383	0.82[ASN][1000 genomes]
rs7986707	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7988864	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7995844	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9285131	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315671	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9315675	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9315678	0.80[GIH][hapmap]
rs9532371	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9532372	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548722	0.84[EUR][1000 genomes]
rs9548729	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548731	0.88[EUR][1000 genomes]
rs9548733	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548738	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9576776	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576777	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs987848	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs957184	LHFP	cis	parietal	SCAN
rs957184	MRPS31	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39904200-39923600	Weak transcription	Ovary	ovary
2	chr13:39910600-39922400	Weak transcription	Aorta	Aorta
3	chr13:39910600-39924400	Weak transcription	Adipose Nuclei	Adipose
4	chr13:39912400-39920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:39912400-39924600	Weak transcription	Fetal Lung	lung
6	chr13:39913000-39920000	Weak transcription	HSMM	muscle
7	chr13:39913200-39919800	Weak transcription	Right Ventricle	heart
8	chr13:39913200-39922400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:39914000-39922400	Weak transcription	Gastric	stomach
10	chr13:39914200-39924400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr13:39914400-39922800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr13:39914600-39916400	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:39914800-39916600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:39914800-39916800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:39914800-39924600	Weak transcription	Fetal Stomach	stomach
16	chr13:39915000-39917200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:39915400-39915800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr13:39915400-39915800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr13:39915400-39915800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr13:39915400-39915800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:39915400-39916000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr13:39915600-39915800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:39915600-39915800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr13:39915600-39916200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:39915600-39918400	Strong transcription	Left Ventricle	heart
26	chr13:39915600-39919800	Weak transcription	Fetal Heart	heart
27	chr13:39915600-39920000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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