Variant report

Variant	rs248724
Chromosome Location	chr5:127039078-127039079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr5:127038738-127039475	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000230561	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10041967	0.97[EUR][1000 genomes]
rs10061252	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1007623	0.97[EUR][1000 genomes]
rs10519953	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1086523	0.96[EUR][1000 genomes]
rs1086524	0.92[EUR][1000 genomes]
rs1086525	0.96[EUR][1000 genomes]
rs1086526	0.96[EUR][1000 genomes]
rs1086527	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1086529	0.96[EUR][1000 genomes]
rs1086530	0.95[EUR][1000 genomes]
rs1086531	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1086532	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1086533	0.96[EUR][1000 genomes]
rs1086534	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1088167	0.96[EUR][1000 genomes]
rs10900792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1092720	0.96[EUR][1000 genomes]
rs11241938	0.96[EUR][1000 genomes]
rs11241939	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11241942	0.81[EUR][1000 genomes]
rs11950864	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs11957799	0.81[EUR][1000 genomes]
rs1213827	0.97[EUR][1000 genomes]
rs1228156	0.85[EUR][1000 genomes]
rs1234542	0.97[EUR][1000 genomes]
rs12652197	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12653785	0.83[EUR][1000 genomes]
rs1432958	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1515640	0.85[EUR][1000 genomes]
rs1560673	0.95[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs173580	0.97[EUR][1000 genomes]
rs173581	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs173582	0.96[EUR][1000 genomes]
rs1816404	0.97[EUR][1000 genomes]
rs1816405	0.97[EUR][1000 genomes]
rs187461	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1897525	0.85[EUR][1000 genomes]
rs193736	0.96[EUR][1000 genomes]
rs248689	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248690	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248691	0.90[EUR][1000 genomes]
rs248692	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248696	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248698	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248700	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248701	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248702	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248706	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248711	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248712	0.96[EUR][1000 genomes]
rs248713	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248715	0.96[EUR][1000 genomes]
rs248716	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248717	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248718	0.97[EUR][1000 genomes]
rs248720	0.96[EUR][1000 genomes]
rs248721	0.96[EUR][1000 genomes]
rs248722	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248730	0.96[EUR][1000 genomes]
rs248731	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248732	0.96[EUR][1000 genomes]
rs248733	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248735	0.96[EUR][1000 genomes]
rs248737	0.95[EUR][1000 genomes]
rs248738	0.96[EUR][1000 genomes]
rs248739	0.96[EUR][1000 genomes]
rs248740	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248741	0.96[EUR][1000 genomes]
rs248742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2569142	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2569144	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569146	0.85[EUR][1000 genomes]
rs2673749	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2673750	0.96[EUR][1000 genomes]
rs2673763	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2673764	0.92[EUR][1000 genomes]
rs2673772	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4340958	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4361571	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs45074	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs54201	0.96[EUR][1000 genomes]
rs59513079	0.85[EUR][1000 genomes]
rs62373501	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62373502	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6595789	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7714847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7736233	0.92[EUR][1000 genomes]
rs790827	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs791071	0.96[EUR][1000 genomes]
rs791072	0.96[EUR][1000 genomes]
rs791073	0.96[EUR][1000 genomes]
rs791074	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs809349	0.96[EUR][1000 genomes]
rs812059	0.89[EUR][1000 genomes]
rs899190	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv830479	chr5:126849254-127053121	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798341	chr5:127038316-127061310	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248724	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127032800-127040800	Weak transcription	NHDF-Ad	bronchial
2	chr5:127033000-127040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:127033000-127040600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:127033000-127041000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:127033800-127040600	Weak transcription	NHLF	lung
6	chr5:127034200-127040800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:127034200-127041000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:127035800-127040600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:127035800-127041000	Weak transcription	Fetal Lung	lung
10	chr5:127035800-127041200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:127036400-127041000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127038200-127039200	Enhancers	Rectal Smooth Muscle	rectum
13	chr5:127038200-127039800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:127038400-127039200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:127038400-127039200	Enhancers	Right Ventricle	heart
16	chr5:127038400-127039400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:127038400-127039400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr5:127038400-127039600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:127038400-127039800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:127038400-127041600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:127038400-127041600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:127038400-127041800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:127038600-127039200	Active TSS	Right Atrium	heart
24	chr5:127038600-127039200	Enhancers	Stomach Smooth Muscle	stomach
25	chr5:127038600-127041800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:127038800-127039200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr5:127038800-127039600	Enhancers	Colon Smooth Muscle	Colon
28	chr5:127038800-127040000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr5:127038800-127041000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:127039000-127039200	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:127039000-127039200	Enhancers	Left Ventricle	heart
32	chr5:127039000-127039400	Enhancers	Fetal Brain Male	brain
33	chr5:127039000-127039800	Enhancers	A549	lung

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