Variant report

Variant	rs3901934
Chromosome Location	chr9:8420576-8420577
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1039337	0.89[CHB][hapmap]
rs10739162	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10758968	0.83[CHB][hapmap]
rs10758972	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758973	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10815866	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815868	0.81[YRI][hapmap]
rs10815870	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10977060	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs12235640	0.83[CHB][hapmap]
rs12235754	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap]
rs13292038	0.89[CHB][hapmap]
rs1359114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1500326	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs1500332	0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs1500333	0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs1535674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535675	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535676	0.83[YRI][hapmap]
rs2031214	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2031215	0.82[YRI][hapmap]
rs2031216	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2031219	1.00[CHB][hapmap]
rs2890778	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847294	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3896024	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742502	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs6477303	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7027844	0.87[CHD][hapmap]
rs7036240	0.89[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap]
rs7039560	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7043664	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7849657	0.88[CHB][hapmap]
rs7856760	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7861870	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs904781	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv613287	chr9:8408453-8422302	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3901934	RLN1	cis	parietal	SCAN
rs3901934	TEX11	trans	cerebellum	SCAN
rs3901934	CDC37L1	cis	cerebellum	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	chr9:8394000-8424400	Weak transcription	Fetal Lung	lung
3	chr9:8402400-8421000	Weak transcription	Brain Hippocampus Middle	brain
4	chr9:8402600-8448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:8402800-8438000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:8405800-8438000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:8408200-8429200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:8410600-8436800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:8415400-8435800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
11	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:8419600-8421200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:8419800-8421200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:8419800-8421200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:8419800-8447600	Weak transcription	Fetal Brain Female	brain
16	chr9:8420000-8422000	Enhancers	Brain Germinal Matrix	brain
17	chr9:8420200-8421400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr9:8420200-8425400	Weak transcription	Brain Substantia Nigra	brain
19	chr9:8420200-8436800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:8420400-8420600	Enhancers	Aorta	Aorta
21	chr9:8420400-8421200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr9:8420400-8421200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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