Variant report

Variant	rs12500834
Chromosome Location	chr4:7400474-7400475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10000132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10000236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10001291	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs10005036	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs10005361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033441	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs10516186	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs12501740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12512241	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]
rs12512986	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13103153	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105667	1.00[CEU][hapmap]
rs13106023	0.81[AFR][1000 genomes]
rs13113743	0.95[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs13125483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13126413	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs13128656	0.81[AFR][1000 genomes]
rs13132744	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13140023	0.81[AFR][1000 genomes]
rs13146595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150726	0.81[AFR][1000 genomes]
rs17758463	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34849258	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36061257	0.81[AFR][1000 genomes]
rs62277574	0.81[AFR][1000 genomes]
rs62277575	0.81[AFR][1000 genomes]
rs68191574	0.81[AFR][1000 genomes]
rs6821857	0.81[AFR][1000 genomes]
rs6835535	0.95[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs6835739	0.81[AFR][1000 genomes]
rs6847931	0.81[AFR][1000 genomes]
rs6852520	0.81[AFR][1000 genomes]
rs6852909	0.81[AFR][1000 genomes]
rs6854113	1.00[CEU][hapmap]
rs7356467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7698559	1.00[ASN][1000 genomes]
rs7700129	1.00[CEU][hapmap]
rs9994834	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs9995355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997320	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs9997426	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9997594	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs9997712	0.93[EUR][1000 genomes]
rs9997796	0.85[CEU][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][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	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003679	chr4:7319111-7449262	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv469758	chr4:7370083-7546250	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv3437934	chr4:7400351-7405049	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7391800-7402000	Enhancers	Brain Germinal Matrix	brain
2	chr4:7393600-7400800	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr4:7396800-7401400	Enhancers	Brain Cingulate Gyrus	brain
4	chr4:7397400-7400800	Enhancers	HSMMtube	muscle
5	chr4:7397400-7401200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:7397400-7401800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:7397600-7401600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:7398200-7400800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:7398400-7401200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:7398600-7400800	Bivalent Enhancer	Fetal Lung	lung
11	chr4:7398800-7400800	Enhancers	Colon Smooth Muscle	Colon
12	chr4:7398800-7401400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr4:7399000-7401200	Enhancers	Fetal Brain Male	brain
14	chr4:7399000-7401400	Enhancers	Brain Angular Gyrus	brain
15	chr4:7399400-7401200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:7399400-7401200	Enhancers	Brain Substantia Nigra	brain
17	chr4:7399400-7401400	Enhancers	Brain Anterior Caudate	brain
18	chr4:7399400-7401400	Enhancers	Brain Hippocampus Middle	brain
19	chr4:7399400-7401600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:7399600-7401800	Enhancers	Fetal Brain Female	brain
21	chr4:7399800-7401000	Enhancers	Fetal Stomach	stomach
22	chr4:7399800-7404200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:7400000-7400600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:7400000-7400800	Enhancers	Stomach Smooth Muscle	stomach
25	chr4:7400000-7400800	Enhancers	HSMM	muscle
26	chr4:7400000-7401000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:7400000-7404800	Weak transcription	Left Ventricle	heart
28	chr4:7400200-7401000	Enhancers	HMEC	breast
29	chr4:7400200-7404800	Weak transcription	Pancreas	Pancrea

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