Variant report

Variant	rs10124428
Chromosome Location	chr9:8836283-8836284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10118318	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120450	0.80[CHB][hapmap]
rs10120478	0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120501	0.80[CHB][hapmap]
rs10120626	0.82[AFR][1000 genomes]
rs10121203	0.80[CHB][hapmap]
rs10121702	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10122784	0.95[YRI][hapmap]
rs10758996	0.80[CHB][hapmap]
rs10758997	0.84[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758998	0.87[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815964	0.80[CHB][hapmap]
rs10815965	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10977314	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1434253	0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1434254	0.80[CHB][hapmap]
rs1434255	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434256	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434258	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434273	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1836227	0.86[ASN][1000 genomes]
rs1836229	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1836230	0.86[ASN][1000 genomes]
rs1836231	0.86[ASN][1000 genomes]
rs1865338	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1972798	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099406	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2570295	0.91[ASN][1000 genomes]
rs2570299	0.93[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2570964	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4372066	0.84[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7024487	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7035236	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048621	0.80[CHB][hapmap]
rs7853143	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7863423	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864464	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864670	0.93[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10124428	KIAA1432	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8822200-8838600	Weak transcription	Osteobl	bone
2	chr9:8823400-8845000	Weak transcription	Fetal Brain Female	brain
3	chr9:8826000-8837400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:8826000-8842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:8832800-8842800	Weak transcription	Fetal Brain Male	brain
6	chr9:8833000-8837400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:8833400-8840800	Weak transcription	Brain Angular Gyrus	brain
8	chr9:8833400-8842800	Weak transcription	Fetal Lung	lung
9	chr9:8833600-8845000	Weak transcription	Fetal Heart	heart
10	chr9:8834200-8839600	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:8834600-8836400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr9:8835000-8837400	Enhancers	Ovary	ovary
13	chr9:8835000-8850800	Weak transcription	Fetal Kidney	kidney
14	chr9:8835200-8842400	Weak transcription	Brain Anterior Caudate	brain
15	chr9:8835200-8842800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:8835200-8843000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:8835200-8852000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:8835200-8852400	Weak transcription	Aorta	Aorta
19	chr9:8835400-8837400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:8835400-8840600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:8835400-8840600	Weak transcription	Brain Substantia Nigra	brain
22	chr9:8835400-8845000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:8835600-8850800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:8835600-8851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:8835800-8842600	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:8835800-8844600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:8835800-8851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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