Variant report

Variant	rs7872026
Chromosome Location	chr9:8816665-8816666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10115341	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511510	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10815959	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10815960	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1434252	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1434257	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1434259	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1434274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836226	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836228	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2099407	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255102	0.82[CHB][hapmap]
rs2570293	0.86[EUR][1000 genomes]
rs2570298	0.88[EUR][1000 genomes]
rs2814723	0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2890828	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890829	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477359	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7028749	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7851333	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7864631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv892240	chr9:8796449-8834108	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv892241	chr9:8805462-8822267	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7872026	TECPR1	trans	cerebellum	SCAN
rs7872026	KIAA1432	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8794200-8821800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8794800-8825600	Weak transcription	Ovary	ovary
3	chr9:8808000-8825600	Weak transcription	Aorta	Aorta
4	chr9:8810600-8822600	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:8814200-8817200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr9:8814200-8817400	Enhancers	Brain Hippocampus Middle	brain
7	chr9:8814200-8817600	Enhancers	Brain Angular Gyrus	brain
8	chr9:8814200-8817800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:8814200-8818400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:8814400-8817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:8814400-8818800	Enhancers	Brain Cingulate Gyrus	brain
12	chr9:8814600-8816800	Enhancers	Liver	Liver
13	chr9:8815200-8817200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:8815200-8817200	Enhancers	Brain Substantia Nigra	brain
15	chr9:8815200-8817400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:8815200-8817600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:8815200-8818000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr9:8815400-8816800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr9:8815400-8817600	Enhancers	Fetal Brain Female	brain
20	chr9:8815400-8818000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:8815600-8817000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:8815600-8817200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:8815600-8817600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:8815600-8817800	Enhancers	Brain Anterior Caudate	brain
25	chr9:8815800-8817200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:8815800-8817200	Enhancers	Fetal Lung	lung
27	chr9:8815800-8817600	Enhancers	Brain Germinal Matrix	brain
28	chr9:8816000-8817200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr9:8816000-8817600	Enhancers	Fetal Kidney	kidney
30	chr9:8816200-8817000	Enhancers	Fetal Heart	heart
31	chr9:8816400-8817200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr9:8816600-8817200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr9:8816600-8817400	Weak transcription	Fetal Brain Male	brain
34	chr9:8816600-8818200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:8816600-8825200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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