Variant report

Variant	rs1880368
Chromosome Location	chr7:69785604-69785605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10229027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10229155	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10234614	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10234844	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234892	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10235487	0.81[ASN][1000 genomes]
rs10235781	0.84[ASN][1000 genomes]
rs10237530	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10237685	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10244275	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10246631	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10251416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10256062	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10258298	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10258962	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10268924	0.85[ASN][1000 genomes]
rs10277411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10280622	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035010	0.81[ASN][1000 genomes]
rs10486874	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486875	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950199	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11766329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12112638	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155138	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698855	0.81[ASN][1000 genomes]
rs12698871	0.85[ASN][1000 genomes]
rs12698895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698899	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13221252	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226923	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13228123	0.81[ASN][1000 genomes]
rs1357759	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1404274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464788	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474368	0.90[ASN][1000 genomes]
rs1524518	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2103132	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2222544	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2280613	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280614	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2866277	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35303761	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846984	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460536	0.81[ASN][1000 genomes]
rs6460537	0.85[ASN][1000 genomes]
rs6460541	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651055	0.85[ASN][1000 genomes]
rs6943555	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950647	0.85[ASN][1000 genomes]
rs6953344	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6954715	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954837	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957740	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6961345	0.85[ASN][1000 genomes]
rs6962999	0.81[ASN][1000 genomes]
rs6967697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6967986	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6969375	0.87[EUR][1000 genomes]
rs6975279	0.85[ASN][1000 genomes]
rs6976581	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781401	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7781727	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7784584	0.83[ASN][1000 genomes]
rs7787612	0.91[EUR][1000 genomes]
rs7790729	0.85[ASN][1000 genomes]
rs7792775	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792964	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7796080	0.85[ASN][1000 genomes]
rs7798991	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7799308	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7805470	0.86[ASN][1000 genomes]
rs8180850	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs870920	0.86[ASN][1000 genomes]
rs873835	0.86[ASN][1000 genomes]
rs9918496	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9918544	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880368	WBSCR17	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69776000-69786600	Enhancers	Primary T cells from cord blood	blood
2	chr7:69778600-69789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:69779600-69802200	Weak transcription	Primary B cells from cord blood	blood
4	chr7:69780800-69785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:69782000-69788000	Weak transcription	Left Ventricle	heart
6	chr7:69782800-69786200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:69782800-69786200	Weak transcription	Gastric	stomach
8	chr7:69782800-69787600	Weak transcription	Fetal Stomach	stomach
9	chr7:69782800-69787800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:69782800-69790400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:69782800-69790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:69783000-69785800	Weak transcription	HMEC	breast
13	chr7:69783000-69790400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:69783400-69785800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:69783800-69785800	Weak transcription	Esophagus	oesophagus
16	chr7:69783800-69787800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:69784400-69790800	Weak transcription	Fetal Thymus	thymus
18	chr7:69784600-69786600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:69785000-69788600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:69785200-69786200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr7:69785200-69786800	Enhancers	Brain Substantia Nigra	brain
22	chr7:69785400-69786000	Enhancers	Brain Anterior Caudate	brain
23	chr7:69785400-69786000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:69785400-69786200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr7:69785400-69786200	Enhancers	Brain Hippocampus Middle	brain
26	chr7:69785400-69786400	Enhancers	Brain Angular Gyrus	brain
27	chr7:69785400-69790400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:69785600-69786200	Enhancers	Brain Cingulate Gyrus	brain
29	chr7:69785600-69786400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr7:69785600-69786800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:69785600-69787200	Enhancers	NHEK	skin

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