Variant report

Variant	rs41537644
Chromosome Location	chr4:79229435-79229436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10008653	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1017649	0.85[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10461146	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12500443	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12501798	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12502139	0.86[AMR][1000 genomes]
rs12502685	0.85[AMR][1000 genomes]
rs12504081	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12505633	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505887	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12506036	0.85[AMR][1000 genomes]
rs12511360	0.86[AMR][1000 genomes]
rs12511808	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12511889	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641094	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13107378	0.86[AMR][1000 genomes]
rs13108102	0.86[AMR][1000 genomes]
rs13114110	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13117388	0.83[GIH][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs13119684	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13136648	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13138795	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13144541	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1454892	0.81[AMR][1000 genomes]
rs1454898	0.86[AMR][1000 genomes]
rs1484344	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17003028	0.84[CEU][hapmap]
rs17455826	0.83[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs1840391	0.88[AMR][1000 genomes]
rs1840392	0.87[AMR][1000 genomes]
rs2124143	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2198635	0.87[AMR][1000 genomes]
rs34535077	0.80[AMR][1000 genomes]
rs345525	0.85[ASN][1000 genomes]
rs345529	0.84[ASN][1000 genomes]
rs34643532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35290872	0.86[AMR][1000 genomes]
rs35291597	0.88[AMR][1000 genomes]
rs35419939	0.87[AMR][1000 genomes]
rs35683023	0.82[AMR][1000 genomes]
rs35828300	0.88[AMR][1000 genomes]
rs425288	0.82[ASN][1000 genomes]
rs4515188	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58101131	0.80[AMR][1000 genomes]
rs62309861	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62310017	0.88[AMR][1000 genomes]
rs62310023	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs62310045	0.87[AMR][1000 genomes]
rs6815945	0.81[EUR][1000 genomes]
rs6854207	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6856362	0.87[AMR][1000 genomes]
rs7656032	0.85[AMR][1000 genomes]
rs7661907	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681247	0.81[AMR][1000 genomes]
rs7686297	0.82[AMR][1000 genomes]
rs7693120	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs943821	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs943822	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2763369	chr4:79229435-79232154	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41537644	PARM1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
3	chr4:79215800-79237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:79215800-79243800	Weak transcription	Right Ventricle	heart
5	chr4:79218600-79230000	Weak transcription	Fetal Kidney	kidney
6	chr4:79220400-79246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:79220400-79246600	Weak transcription	HMEC	breast
8	chr4:79220600-79229800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:79220600-79234200	Weak transcription	HSMMtube	muscle
10	chr4:79220600-79241400	Weak transcription	Aorta	Aorta
11	chr4:79220800-79243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:79221000-79237400	Weak transcription	Fetal Heart	heart
13	chr4:79221000-79240000	Weak transcription	Psoas Muscle	Psoas
14	chr4:79221200-79229800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:79221200-79229800	Weak transcription	Fetal Lung	lung
16	chr4:79221200-79231200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:79221200-79232600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:79227000-79241400	Weak transcription	Left Ventricle	heart
20	chr4:79228600-79229800	Strong transcription	Fetal Intestine Small	intestine
21	chr4:79228800-79230000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:79229000-79229600	Genic enhancers	H1 Cell Line	embryonic stem cell
23	chr4:79229000-79229600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:79229000-79229800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:79229000-79231000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:79229000-79232000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:79229000-79233200	Strong transcription	HepG2	liver
28	chr4:79229200-79229600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr4:79229200-79229800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:79229200-79229800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
31	chr4:79229200-79229800	Strong transcription	Fetal Stomach	stomach
32	chr4:79229200-79230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:79229200-79230000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:79229200-79230000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:79229200-79230800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:79229200-79231200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:79229200-79233200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:79229400-79229800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:79229400-79231800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:79229400-79241000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:79229400-79241200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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