Variant report

Variant	rs9886302
Chromosome Location	chr7:70751484-70751485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10226199	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10231965	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10256635	0.82[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs10261998	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10263619	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10266560	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272997	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11976781	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12155368	0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12668780	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs12669285	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12673556	0.85[JPT][hapmap]
rs1465231	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1558003	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1574440	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs1922527	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2141885	0.85[JPT][hapmap]
rs2527289	0.85[JPT][hapmap]
rs2527297	0.84[JPT][hapmap]
rs2527298	0.85[JPT][hapmap]
rs2527312	0.85[JPT][hapmap]
rs28631036	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670821	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867411	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28799658	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923571	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4073529	0.89[JPT][hapmap]
rs4446620	0.92[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6460649	0.85[EUR][1000 genomes]
rs67615560	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942815	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943983	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6961808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976562	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976574	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73177835	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73179792	0.82[EUR][1000 genomes]
rs73356099	0.80[EUR][1000 genomes]
rs7778324	0.85[JPT][hapmap]
rs7792223	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638618	0.85[GIH][hapmap]
rs9690269	0.85[YRI][hapmap];0.83[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	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1033155	chr7:70712368-70757929	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9886302	STAG3L4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70732400-70755400	Weak transcription	Right Atrium	heart
2	chr7:70740000-70751600	Weak transcription	Left Ventricle	heart
3	chr7:70745800-70755000	Weak transcription	Fetal Heart	heart
4	chr7:70748000-70751600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:70749800-70752000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:70750000-70751600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:70750000-70751800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:70750000-70752200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:70750200-70751800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr7:70750200-70752200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:70750200-70752200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:70750200-70752200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:70750400-70751600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr7:70750400-70751600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:70750400-70751600	Enhancers	HSMM	muscle
16	chr7:70750400-70752000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:70750600-70752200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:70750600-70752400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:70750600-70752600	Enhancers	Fetal Muscle Leg	muscle
20	chr7:70750600-70752800	Enhancers	Fetal Lung	lung
21	chr7:70750800-70751800	Weak transcription	Fetal Stomach	stomach
22	chr7:70750800-70752600	Enhancers	Colon Smooth Muscle	Colon
23	chr7:70751000-70751600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:70751000-70751800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr7:70751000-70751800	Enhancers	Rectal Smooth Muscle	rectum
26	chr7:70751000-70751800	Enhancers	Stomach Smooth Muscle	stomach
27	chr7:70751000-70752200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr7:70751200-70752000	Enhancers	Brain Hippocampus Middle	brain
29	chr7:70751200-70752600	Enhancers	Ovary	ovary
30	chr7:70751200-70755400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:70751200-70768200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:70751400-70751600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:70751400-70751800	Enhancers	H9 Cell Line	embryonic stem cell
34	chr7:70751400-70751800	Enhancers	Brain Cingulate Gyrus	brain
35	chr7:70751400-70751800	Enhancers	Brain Germinal Matrix	brain
36	chr7:70751400-70752000	Enhancers	Brain Substantia Nigra	brain
37	chr7:70751400-70752200	Enhancers	Brain Angular Gyrus	brain
38	chr7:70751400-70752200	Enhancers	Fetal Muscle Trunk	muscle
39	chr7:70751400-70752600	Enhancers	Fetal Kidney	kidney
40	chr7:70751400-70752800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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