Variant report

Variant	rs28495699
Chromosome Location	chr4:7474258-7474259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10004803	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10012386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10012715	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026218	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10937822	0.87[EUR][1000 genomes]
rs10937823	0.89[EUR][1000 genomes]
rs11736890	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11736935	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11736976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11736984	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12499417	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12499489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12503258	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12503401	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12504152	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12506763	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12507811	0.84[EUR][1000 genomes]
rs12508570	0.89[EUR][1000 genomes]
rs13119088	0.89[EUR][1000 genomes]
rs13138627	0.89[EUR][1000 genomes]
rs13139074	0.89[EUR][1000 genomes]
rs16840313	0.95[ASN][1000 genomes]
rs16840336	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16840339	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16840348	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16840358	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1807425	0.83[ASN][1000 genomes]
rs28361965	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28393125	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28479426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493186	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28494591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578475	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28630370	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705151	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28726347	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34091365	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34517145	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34862495	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35085269	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35119395	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35685691	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35723054	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36110997	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4234814	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4266295	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71601843	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71601844	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71601845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7683874	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	nsv878560	chr4:7402284-7475114	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv878561	chr4:7402284-7544610	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv878563	chr4:7420785-7529367	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878564	chr4:7421007-7535214	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878566	chr4:7456717-7529367	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
11	nsv878567	chr4:7456717-7544610	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv520804	chr4:7473863-7475114	Enhancers Bivalent Enhancer Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7471600-7480600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr4:7472400-7475000	Weak transcription	Brain Anterior Caudate	brain
3	chr4:7473200-7476000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:7473400-7475400	Enhancers	Brain Germinal Matrix	brain
5	chr4:7473600-7474600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:7473600-7474600	Bivalent Enhancer	Fetal Stomach	stomach
7	chr4:7473600-7475200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:7473600-7475200	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr4:7473600-7475400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:7473800-7474600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:7473800-7475200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:7473800-7475200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:7473800-7475400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:7474000-7474600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:7474000-7474800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:7474000-7474800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr4:7474000-7474800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:7474000-7475000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr4:7474200-7475000	Enhancers	HUES48 Cell Line	embryonic stem cell

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