Variant report

Variant	rs325419
Chromosome Location	chr12:32572460-32572461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32551367..32553605-chr12:32570827..32573292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1045751	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771942	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771943	0.81[ASN][1000 genomes]
rs10844197	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844198	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1128591	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12367488	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs167806	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186568	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs188979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062600	0.96[ASN][1000 genomes]
rs2253235	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2253237	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2253247	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2450506	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455004	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455005	0.83[EUR][1000 genomes]
rs2632326	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2632330	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632337	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2632363	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2651365	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2651366	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651367	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651368	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651371	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2651372	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2651374	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2651375	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2651376	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2651377	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651380	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2728675	0.96[ASN][1000 genomes]
rs2728676	0.94[ASN][1000 genomes]
rs2728678	0.94[ASN][1000 genomes]
rs2728679	0.90[ASN][1000 genomes]
rs2728681	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2728689	0.93[ASN][1000 genomes]
rs2728690	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733683	0.92[ASN][1000 genomes]
rs2733694	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733696	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733698	0.91[ASN][1000 genomes]
rs2733703	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2733704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2733705	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2931554	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs325418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325420	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325421	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325423	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325424	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931622	0.96[ASN][1000 genomes]
rs4931624	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931625	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs56146365	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61927173	0.81[ASN][1000 genomes]
rs7298319	0.81[EUR][1000 genomes]
rs7298381	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7312698	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315762	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315797	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7963401	0.90[AFR][1000 genomes];0.96[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs325419	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32553600-32572600	Weak transcription	Esophagus	oesophagus
2	chr12:32554200-32573800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:32571200-32572600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:32571200-32573400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr12:32571200-32573400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:32571200-32573400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:32571200-32573400	Enhancers	Placenta	Placenta
9	chr12:32571200-32573600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr12:32571400-32572800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:32571400-32572800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:32571400-32572800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:32571400-32573000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr12:32571400-32573200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:32571400-32573400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:32571400-32573400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:32571400-32573400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr12:32571400-32573400	Enhancers	Stomach Mucosa	stomach
19	chr12:32571600-32572600	Strong transcription	Fetal Intestine Small	intestine
20	chr12:32571600-32572800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:32571600-32573200	Enhancers	HMEC	breast
22	chr12:32571600-32573400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:32571600-32573400	Enhancers	Adipose Nuclei	Adipose
24	chr12:32571600-32573400	Enhancers	Left Ventricle	heart
25	chr12:32571600-32573400	Enhancers	Pancreas	Pancrea
26	chr12:32571600-32573600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:32571600-32573600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr12:32571600-32573600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:32571600-32573600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:32571600-32573800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:32571600-32574800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:32571600-32576800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:32571800-32572800	Enhancers	Liver	Liver
34	chr12:32571800-32573000	Enhancers	Ovary	ovary
35	chr12:32571800-32573000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:32571800-32573200	Enhancers	Lung	lung
37	chr12:32571800-32573200	Enhancers	Right Atrium	heart
38	chr12:32571800-32573400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr12:32571800-32574200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:32572000-32572600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr12:32572000-32572600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:32572000-32572800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:32572000-32573200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr12:32572000-32573400	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:32572000-32573400	Enhancers	A549	lung
46	chr12:32572000-32573600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:32572000-32573600	Enhancers	Gastric	stomach
48	chr12:32572200-32572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr12:32572200-32572600	Enhancers	Stomach Smooth Muscle	stomach
50	chr12:32572200-32572800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links