Variant report

Variant	rs2107992
Chromosome Location	chr7:79027730-79027731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10253616	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10499842	0.89[JPT][hapmap];0.90[YRI][hapmap]
rs1100309	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs11763567	0.83[JPT][hapmap];0.90[YRI][hapmap]
rs12154356	0.80[YRI][hapmap]
rs1528261	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs17152290	0.92[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs17152314	0.92[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs17152336	0.83[CEU][hapmap]
rs17152352	0.83[EUR][1000 genomes]
rs17152454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17152496	0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs17152499	0.83[ASN][1000 genomes]
rs17152506	0.93[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]
rs2069132	0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs2158707	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242505	0.81[YRI][hapmap]
rs2364912	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35003046	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3884514	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4727838	0.81[YRI][hapmap]
rs55739903	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56011939	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56191332	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56410623	0.83[EUR][1000 genomes]
rs57763664	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59169073	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61046785	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466593	0.84[YRI][hapmap]
rs66627069	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66784949	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66878128	0.83[EUR][1000 genomes]
rs66930031	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67038446	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67145529	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67627178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67945427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68016561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68156712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953105	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6956190	0.92[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs73147403	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73147408	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73147474	0.80[ASN][1000 genomes]
rs73156055	0.83[EUR][1000 genomes]
rs73156080	0.83[EUR][1000 genomes]
rs73704183	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7456505	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7456591	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7797165	0.89[ASW][hapmap];0.91[CEU][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs848909	0.90[JPT][hapmap]
rs848915	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs848958	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs860246	0.82[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs9640776	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9641579	0.92[CEU][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs9641582	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9641583	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9641589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs980354	0.86[CHB][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464600	chr7:78981719-79030922	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv607663	chr7:78981719-79030922	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv888514	chr7:78987060-79061837	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv607664	chr7:78998409-79057761	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv607665	chr7:79027730-79063644	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2107992	RHBDD2	cis	parietal	SCAN
rs2107992	LOC402560	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79017600-79030400	Weak transcription	Brain Substantia Nigra	brain
2	chr7:79026800-79028000	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr7:79026800-79028000	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr7:79027000-79028000	Enhancers	Brain Anterior Caudate	brain
5	chr7:79027000-79028400	Enhancers	HUVEC	blood vessel
6	chr7:79027200-79027800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:79027200-79028200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:79027400-79027800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:79027400-79027800	Enhancers	Adipose Nuclei	Adipose
10	chr7:79027400-79027800	Enhancers	Right Atrium	heart
11	chr7:79027400-79027800	Enhancers	NHDF-Ad	bronchial
12	chr7:79027400-79028000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:79027400-79028000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:79027400-79028000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:79027400-79028000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:79027400-79028000	Enhancers	Brain Cingulate Gyrus	brain
17	chr7:79027400-79028200	Enhancers	NHLF	lung
18	chr7:79027400-79028200	Enhancers	Osteobl	bone
19	chr7:79027400-79028400	Enhancers	Brain Hippocampus Middle	brain
20	chr7:79027600-79027800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr7:79027600-79027800	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr7:79027600-79028000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr7:79027600-79028000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr7:79027600-79028000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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