Variant report

Variant	rs2381798
Chromosome Location	chr9:8431163-8431164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10739162	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs10758973	0.81[AMR][1000 genomes]
rs10815867	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs10815868	0.96[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10815870	0.82[AMR][1000 genomes]
rs10815871	0.91[AMR][1000 genomes]
rs1500327	0.81[GIH][hapmap]
rs1535676	0.89[CEU][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes]
rs16927858	0.85[JPT][hapmap]
rs2031214	0.81[AMR][1000 genomes]
rs2031215	0.96[CEU][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2031216	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs2031218	0.81[JPT][hapmap]
rs2279776	0.81[CEU][hapmap]
rs2381796	0.81[JPT][hapmap]
rs6477303	0.82[AMR][1000 genomes]
rs6477304	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6477305	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6477306	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7467813	0.85[AMR][1000 genomes]
rs7856760	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs7869156	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs942174	0.87[AMR][1000 genomes]
rs942175	0.88[AMR][1000 genomes]
rs942176	0.92[CEU][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes]
rs942177	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2381798	RLN1	cis	parietal	SCAN

Chromatin state (count:35 , 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	chr9:8410600-8436800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:8415400-8435800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
8	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:8419800-8447600	Weak transcription	Fetal Brain Female	brain
10	chr9:8420200-8436800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:8420600-8466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
13	chr9:8421200-8432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:8421400-8456400	Weak transcription	Ovary	ovary
15	chr9:8422000-8464800	Weak transcription	Brain Germinal Matrix	brain
16	chr9:8423200-8446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
18	chr9:8424600-8437800	Weak transcription	Fetal Heart	heart
19	chr9:8425600-8447600	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:8427400-8432600	Enhancers	Primary T cells from cord blood	blood
21	chr9:8428000-8447400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:8429400-8431600	Weak transcription	Primary B cells from cord blood	blood
23	chr9:8429600-8434400	Weak transcription	Fetal Lung	lung
24	chr9:8429800-8432400	Weak transcription	Dnd41	blood
25	chr9:8430000-8431200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:8430000-8436600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:8430200-8465000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:8430800-8431400	Enhancers	Brain Hippocampus Middle	brain
29	chr9:8431000-8431200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:8431000-8431400	Enhancers	Brain Angular Gyrus	brain
31	chr9:8431000-8431400	Enhancers	Thymus	Thymus
32	chr9:8431000-8432000	Enhancers	Brain Substantia Nigra	brain
33	chr9:8431000-8432200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:8431000-8432600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr9:8431000-8432600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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