Variant report

Variant	rs10938844
Chromosome Location	chr4:21554837-21554838
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11935160	0.85[CEU][hapmap]
rs11943551	0.85[CEU][hapmap]
rs11947661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644013	0.88[CEU][hapmap]
rs12651393	0.80[AMR][1000 genomes]
rs13133651	0.85[CEU][hapmap]
rs1380812	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs1460472	0.82[EUR][1000 genomes]
rs1460473	0.86[ASN][1000 genomes]
rs17549122	0.80[ASN][1000 genomes]
rs1824472	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2199286	0.85[CEU][hapmap]
rs2202313	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2323068	0.86[CHB][hapmap]
rs28636012	0.80[ASN][1000 genomes]
rs28694887	0.85[ASN][1000 genomes]
rs28698363	0.83[ASN][1000 genomes]
rs358825	0.83[ASN][1000 genomes]
rs358826	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs358836	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs6448057	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6448063	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs7655166	0.96[CEU][hapmap]
rs972288	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv829879	chr4:21418568-21611002	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv998481	chr4:21421945-21608805	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv829880	chr4:21492426-21693816	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv997742	chr4:21515920-21575213	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1002353	chr4:21518045-21575213	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv1001219	chr4:21518045-21580423	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
8	esv2760860	chr4:21518045-21580435	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
9	nsv525271	chr4:21519577-21575623	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
10	nsv470019	chr4:21519577-21576754	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
11	nsv593805	chr4:21519577-21576754	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv1009425	chr4:21542141-21566178	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	nsv593806	chr4:21546537-21566178	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10938844	MED28	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21553800-21557000	Enhancers	Fetal Heart	heart
2	chr4:21554400-21555800	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr4:21554400-21557000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:21554400-21557000	Enhancers	Fetal Brain Female	brain
5	chr4:21554600-21555200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:21554600-21555200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:21554600-21555400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:21554600-21555800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:21554600-21555800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:21554600-21556000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr4:21554600-21556000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:21554600-21557800	Enhancers	Fetal Brain Male	brain
13	chr4:21554800-21556400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr4:21554800-21566200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links