Variant report

Variant	rs1356875
Chromosome Location	chr3:46668689-46668690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11130099	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130102	0.90[JPT][hapmap]
rs11719679	0.85[JPT][hapmap]
rs11922418	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12491236	0.85[JPT][hapmap]
rs12491294	0.85[JPT][hapmap]
rs13083665	0.82[ASN][1000 genomes]
rs4683253	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683260	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6773430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643859	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876738	chr3:46639048-46680063	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1356875	PTH1R	cis	parietal	SCAN
rs1356875	LRRC2	cis	cerebellum	SCAN
rs1356875	ATRIP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46651600-46671200	Weak transcription	Right Atrium	heart
2	chr3:46661600-46670200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:46661800-46670200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:46662200-46670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:46666200-46669200	Enhancers	Fetal Intestine Large	intestine
6	chr3:46666600-46669200	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr3:46666600-46669200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:46666600-46669400	Enhancers	Fetal Intestine Small	intestine
9	chr3:46666600-46670800	Enhancers	Fetal Muscle Leg	muscle
10	chr3:46667000-46669400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:46667000-46669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:46667000-46669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:46667000-46670000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:46667000-46670000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:46667000-46670000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:46667000-46670000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:46667000-46670000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:46667200-46669800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:46667200-46669800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:46667200-46670000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:46667400-46669200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:46667400-46669400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:46667600-46668800	Enhancers	Fetal Kidney	kidney
24	chr3:46667600-46669800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:46667600-46671200	Weak transcription	Left Ventricle	heart
26	chr3:46667800-46671200	Enhancers	Fetal Stomach	stomach
27	chr3:46668000-46669200	Enhancers	Colonic Mucosa	Colon
28	chr3:46668000-46672400	Enhancers	Placenta	Placenta
29	chr3:46668600-46669200	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links