Variant report

Variant	rs2279757
Chromosome Location	chr7:65828663-65828664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65828611..65830328-chr7:65850257..65852199,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10261710	0.95[EUR][1000 genomes]
rs1065265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950029	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10950035	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950036	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10950040	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11763224	0.87[EUR][1000 genomes]
rs11766183	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767262	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11769702	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11770063	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12667200	0.87[ASN][1000 genomes]
rs12668269	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12670811	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12671152	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12672427	0.92[EUR][1000 genomes]
rs1547529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17138149	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs17138156	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1862085	0.88[EUR][1000 genomes]
rs1909508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2173571	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420612	0.87[EUR][1000 genomes]
rs35459055	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs3936065	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718325	0.93[EUR][1000 genomes]
rs4718335	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718346	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718348	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4718364	0.85[EUR][1000 genomes]
rs6460281	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460298	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66594357	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67775320	0.87[EUR][1000 genomes]
rs6945896	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6950988	0.88[EUR][1000 genomes]
rs6960848	0.91[EUR][1000 genomes]
rs6961853	0.85[EUR][1000 genomes]
rs6969224	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970498	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6979636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73142233	0.93[EUR][1000 genomes]
rs73142245	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73142265	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73146609	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73148639	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73148689	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73150604	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73152714	0.85[EUR][1000 genomes]
rs7782212	0.91[EUR][1000 genomes]
rs7783889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7785117	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7786735	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7801332	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7810213	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7811204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2279757	GS1-124K5.4	cis	Stomach	GTEx
rs2279757	RABGEF1	cis	parietal	SCAN
rs2279757	GS1-124K5.11	cis	Thyroid	GTEx
rs2279757	ZNF273	cis	cerebellum	SCAN
rs2279757	GUSB	cis	parietal	SCAN
rs2279757	RNU6-96P	cis	Thyroid	GTEx
rs2279757	GTF2IRD1P1	cis	Thyroid	GTEx
rs2279757	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2279757	RABGEF1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65805200-65843600	Weak transcription	Aorta	Aorta
2	chr7:65814000-65843800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:65817400-65842600	Weak transcription	Gastric	stomach
5	chr7:65817600-65828800	Weak transcription	Ovary	ovary
6	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
9	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
10	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:65822000-65831800	Weak transcription	HSMM	muscle
13	chr7:65822000-65843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:65822200-65828800	Weak transcription	Osteobl	bone
15	chr7:65822400-65831400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:65822400-65831400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:65822800-65839200	Weak transcription	Fetal Intestine Small	intestine
18	chr7:65822800-65841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:65823400-65843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:65824000-65831200	Weak transcription	Fetal Lung	lung
21	chr7:65824800-65843600	Weak transcription	Esophagus	oesophagus
22	chr7:65825000-65828800	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:65825000-65833800	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:65825000-65844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:65825200-65831200	Weak transcription	NHDF-Ad	bronchial
26	chr7:65825200-65841200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:65825200-65841200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:65825200-65842200	Weak transcription	Spleen	Spleen
29	chr7:65825200-65844200	Weak transcription	NHLF	lung
30	chr7:65826200-65842600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:65826400-65829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:65826400-65842400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:65826400-65842800	Weak transcription	Liver	Liver
34	chr7:65826600-65841200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:65826800-65830800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:65826800-65830800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:65826800-65838800	Weak transcription	Placenta	Placenta
38	chr7:65826800-65839800	Weak transcription	Fetal Stomach	stomach
39	chr7:65827000-65843800	Weak transcription	NHEK	skin
40	chr7:65827400-65831600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:65827400-65841200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:65827600-65830600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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