Variant report

Variant	rs325417
Chromosome Location	chr12:32574217-32574218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BICD1-3	chr12:32573758-32574475	NONHSAT027612

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1055876	0.82[CEU][hapmap]
rs10844200	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10844201	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12229856	0.82[CEU][hapmap]
rs1500874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1809912	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1809913	0.82[ASN][1000 genomes]
rs1872829	0.87[CEU][hapmap]
rs2062602	0.87[ASN][1000 genomes]
rs2088806	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088807	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389036	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2467065	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470382	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2651360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2651361	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2651362	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2651363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2651369	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2651378	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2651379	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2728669	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2728671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2728673	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2728674	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2728680	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2728682	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2728683	0.93[ASN][1000 genomes]
rs2728684	0.97[ASN][1000 genomes]
rs2728713	0.81[AMR][1000 genomes]
rs2733682	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958117	0.95[ASN][1000 genomes]
rs6488050	0.82[CEU][hapmap]
rs6488051	0.87[CEU][hapmap]
rs7296118	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904917	0.82[ASN][1000 genomes]
rs950079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs950080	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs950081	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs950082	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv469346	chr12:32531220-32587465	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558188	chr12:32531220-32587465	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv469347	chr12:32555846-32602079	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv558189	chr12:32555846-32602079	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:32571600-32574800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:32571600-32576800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr12:32572600-32574600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:32572600-32574600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32572600-32575800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:32572800-32575400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:32572800-32575400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:32572800-32575600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:32573000-32575600	Weak transcription	NHEK	skin
11	chr12:32573000-32576800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:32573000-32577600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:32573000-32582200	Weak transcription	Ovary	ovary
14	chr12:32573200-32575400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:32573200-32575600	Weak transcription	HMEC	breast
16	chr12:32573400-32574400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:32573400-32575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:32573400-32575600	Weak transcription	Adipose Nuclei	Adipose
19	chr12:32573400-32575600	Weak transcription	A549	lung
20	chr12:32573400-32575800	Weak transcription	Stomach Mucosa	stomach
21	chr12:32573400-32576000	Weak transcription	Placenta	Placenta
22	chr12:32573400-32582000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:32573400-32582400	Weak transcription	Pancreas	Pancrea
24	chr12:32573400-32583600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:32573400-32587000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:32573400-32593400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:32573600-32574400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:32573600-32574400	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:32573600-32575200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:32573600-32575400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:32573800-32574400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:32573800-32574800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:32573800-32575200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:32574000-32574600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:32574000-32574600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:32574000-32574800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr12:32574000-32574800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:32574200-32574400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:32574200-32574600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:32574200-32574800	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links