Variant report

Variant	rs2031214
Chromosome Location	chr9:8425422-8425423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1039337	0.89[CHB][hapmap]
rs10739162	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739163	0.82[ASN][1000 genomes]
rs10758968	0.83[CHB][hapmap]
rs10758972	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10758973	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815866	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10815868	0.84[AMR][1000 genomes]
rs10815870	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815871	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10977060	0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12235640	0.83[CHB][hapmap]
rs12235754	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs13292038	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1359114	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1500326	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs1500332	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs1500333	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs1535674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535676	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2031215	0.83[AMR][1000 genomes]
rs2031216	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031217	0.93[ASN][1000 genomes]
rs2031219	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2381798	0.81[AMR][1000 genomes]
rs2890778	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3847294	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3896024	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3901934	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs3908434	0.85[ASN][1000 genomes]
rs4742500	0.89[ASN][1000 genomes]
rs4742502	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs6477303	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477304	0.83[AMR][1000 genomes]
rs6477305	0.84[AMR][1000 genomes]
rs6477306	0.84[AMR][1000 genomes]
rs7027844	0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7036240	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs7039560	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7043664	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7047641	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7849657	0.88[CHB][hapmap]
rs7856760	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7861870	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869156	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs904781	0.89[CHB][hapmap];0.97[CHD][hapmap]

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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2031214	CDC37L1	cis	cerebellum	SCAN
rs2031214	RLN1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8402600-8448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:8402800-8438000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:8405800-8438000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:8408200-8429200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:8410600-8436800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:8415400-8435800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
9	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:8419800-8447600	Weak transcription	Fetal Brain Female	brain
11	chr9:8420200-8436800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:8420600-8466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
14	chr9:8421200-8432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:8421400-8456400	Weak transcription	Ovary	ovary
16	chr9:8422000-8464800	Weak transcription	Brain Germinal Matrix	brain
17	chr9:8423200-8446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
19	chr9:8424600-8437800	Weak transcription	Fetal Heart	heart
20	chr9:8424800-8425600	Enhancers	Fetal Muscle Leg	muscle
21	chr9:8425000-8429200	Weak transcription	Fetal Lung	lung
22	chr9:8425400-8426200	Enhancers	Brain Substantia Nigra	brain

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