Variant report

Variant	rs7853112
Chromosome Location	chr9:8332353-8332354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10511491	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10732364	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10733545	0.82[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs10733546	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739155	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10739156	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10739157	0.91[CHB][hapmap]
rs10739158	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs10739159	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs10739160	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10758956	0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10758957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10758958	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10758959	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10758963	0.87[CHB][hapmap]
rs10815823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10815826	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10815827	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10815828	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs10815832	0.91[CHB][hapmap]
rs10976970	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10976987	0.95[CHB][hapmap]
rs10976989	0.86[CHB][hapmap];0.81[YRI][hapmap]
rs10977006	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs11543915	0.81[EUR][1000 genomes]
rs11794527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12238805	0.90[ASN][1000 genomes]
rs12682837	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1392518	0.83[CHB][hapmap]
rs1500321	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1500322	0.83[CHB][hapmap]
rs1500323	0.83[CHB][hapmap]
rs1587485	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16927668	0.87[CHB][hapmap]
rs28891834	0.97[ASN][1000 genomes]
rs3736381	0.90[CHB][hapmap]
rs3765142	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[ASN][1000 genomes]
rs3765143	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3780337	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847290	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4740935	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4740936	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4740937	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4740939	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4740940	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4740941	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4742483	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4742485	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4742490	0.87[CHB][hapmap];0.84[GIH][hapmap]
rs7032880	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7848626	0.82[JPT][hapmap]
rs7850069	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851892	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7856860	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7856922	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7857177	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7864500	0.91[CHB][hapmap]
rs7873177	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[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	nsv892224	chr9:8263737-8338431	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7853112	SLC1A1	cis	parietal	SCAN
rs7853112	CD274	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8312200-8338200	Weak transcription	Brain Angular Gyrus	brain
2	chr9:8323400-8341600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:8323800-8341600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:8324000-8345000	Weak transcription	Fetal Brain Male	brain
5	chr9:8324400-8337400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:8326800-8337400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:8327200-8338000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:8328000-8338000	Weak transcription	Dnd41	blood
9	chr9:8328200-8338600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:8328800-8338200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:8329800-8339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:8330000-8337800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:8330000-8338000	Weak transcription	Liver	Liver
14	chr9:8330000-8338600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:8330000-8348600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:8330200-8337400	Weak transcription	Pancreas	Pancrea
17	chr9:8330200-8337800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:8330200-8337800	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:8330200-8337800	Weak transcription	Ovary	ovary
20	chr9:8330200-8338600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:8330200-8339800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:8330200-8339800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:8330200-8340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:8330200-8340400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:8330200-8340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:8330200-8342200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:8330200-8364200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:8330400-8337400	Weak transcription	Fetal Brain Female	brain
29	chr9:8330400-8337600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:8330400-8338200	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:8330400-8338200	Weak transcription	Fetal Stomach	stomach
32	chr9:8330400-8340000	Weak transcription	Placenta	Placenta
33	chr9:8330600-8333000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:8330600-8337400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:8331200-8337400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:8331400-8333200	Strong transcription	Fetal Lung	lung
37	chr9:8331400-8342000	Weak transcription	Fetal Kidney	kidney
38	chr9:8331600-8333200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:8331600-8333800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:8331800-8333200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:8332200-8332600	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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