Variant report

Variant	rs11051938
Chromosome Location	chr12:32482816-32482817
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32479517..32482487-chr12:32482791..32485534,3	K562	blood:

Variant related genes	Relation type
ENSG00000151746	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10431225	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431283	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844179	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10844183	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844184	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10844188	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051925	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051928	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051929	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051932	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11051934	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11051935	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11051936	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051937	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051941	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051943	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051944	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051945	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051946	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11536026	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11833592	0.91[EUR][1000 genomes]
rs12578899	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972033	0.89[EUR][1000 genomes]
rs1972438	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2036304	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270786	0.91[EUR][1000 genomes]
rs2291420	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291421	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388988	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388989	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2728698	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2892655	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748275	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748276	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816819	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4316592	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4474533	0.91[EUR][1000 genomes]
rs4540912	0.90[ASN][1000 genomes]
rs4604975	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931012	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931621	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58236386	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58926489	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58959894	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60221824	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6488044	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300646	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956708	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962680	0.92[EUR][1000 genomes]
rs7963887	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972023	0.86[EUR][1000 genomes]
rs7974653	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977938	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	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	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11051938	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32449600-32490200	Weak transcription	HSMMtube	muscle
2	chr12:32457200-32494400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:32460400-32514600	Weak transcription	HMEC	breast
4	chr12:32472600-32489200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:32472800-32493600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:32475000-32490200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:32475400-32500200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:32475600-32483200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:32475600-32532400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:32475800-32492000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:32475800-32495800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:32475800-32502200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:32475800-32512200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:32476400-32505600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:32476400-32515400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:32476600-32487200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:32476600-32493400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:32477200-32490400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:32477200-32500800	Weak transcription	Hela-S3	cervix
20	chr12:32478400-32490400	Weak transcription	NHLF	lung
21	chr12:32478600-32484600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:32478600-32490200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:32478600-32490400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:32478800-32483600	Weak transcription	A549	lung
25	chr12:32478800-32490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:32478800-32490400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:32478800-32498800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:32479000-32483800	Weak transcription	Placenta	Placenta
29	chr12:32479000-32493600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:32479200-32492400	Weak transcription	Small Intestine	intestine
31	chr12:32479200-32502200	Weak transcription	NHDF-Ad	bronchial
32	chr12:32479200-32504200	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:32479400-32490400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:32479400-32494400	Weak transcription	Right Ventricle	heart
35	chr12:32479400-32501200	Weak transcription	Fetal Brain Male	brain
36	chr12:32479600-32483000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32479600-32483200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:32479600-32483600	Weak transcription	HUVEC	blood vessel
39	chr12:32479600-32491800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:32479800-32483200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:32479800-32485400	Weak transcription	Fetal Kidney	kidney
42	chr12:32480000-32483000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:32480200-32483000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:32480200-32483200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:32480200-32483200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:32480200-32483600	Weak transcription	NHEK	skin
47	chr12:32480200-32484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:32480200-32494000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:32480400-32483000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:32480400-32483000	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links