Variant report

Variant	rs2270438
Chromosome Location	chr12:4549019-4549020
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1019398	0.83[CEU][hapmap]
rs11608707	0.82[CEU][hapmap]
rs2241279	0.80[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2241280	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs2241281	0.91[CHB][hapmap]
rs2241282	0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs2241283	0.82[CEU][hapmap]
rs2270437	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2970827	0.95[CHB][hapmap];0.92[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898616	chr12:4490059-4564613	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585	chr12:4514249-4559242	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2270438	FOXJ2	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4542600-4550400	Weak transcription	Right Atrium	heart
2	chr12:4543200-4549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:4544400-4549200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:4545000-4549600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:4547400-4549600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:4547400-4550000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:4548000-4549200	Enhancers	GM12878-XiMat	blood
8	chr12:4548000-4549400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:4548000-4549600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr12:4548000-4549800	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:4548000-4550000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr12:4548000-4550600	Enhancers	Dnd41	blood
13	chr12:4548000-4551600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:4548200-4550400	Enhancers	Primary B cells from cord blood	blood
15	chr12:4548200-4552400	Enhancers	Fetal Muscle Leg	muscle
16	chr12:4548400-4550400	Weak transcription	Fetal Brain Male	brain
17	chr12:4548400-4550600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:4548400-4553400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:4548400-4553600	Enhancers	Fetal Thymus	thymus
20	chr12:4548600-4549200	Enhancers	Primary T cells from cord blood	blood
21	chr12:4548600-4549200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr12:4548600-4549800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr12:4548600-4549800	Enhancers	HSMM	muscle
24	chr12:4548600-4550400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:4548600-4550600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr12:4548600-4552400	Enhancers	H9 Cell Line	embryonic stem cell
27	chr12:4548600-4554800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr12:4548800-4549200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:4548800-4549400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr12:4548800-4549800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr12:4549000-4549200	Enhancers	Left Ventricle	heart
32	chr12:4549000-4549200	Enhancers	Lung	lung
33	chr12:4549000-4549400	Enhancers	Psoas Muscle	Psoas
34	chr12:4549000-4549800	Enhancers	Fetal Muscle Trunk	muscle
35	chr12:4549000-4549800	Bivalent Enhancer	Placenta	Placenta
36	chr12:4549000-4550400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:4549000-4550400	Weak transcription	HSMMtube	muscle
38	chr12:4549000-4550600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr12:4549000-4551000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:4549000-4552000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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