Variant report

Variant	rs2270786
Chromosome Location	chr12:32490764-32490765
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	chr12:32486141..32488107-chr12:32489173..32490797,2	K562	blood:

Variant related genes	Relation type
ENSG00000151746	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10431225	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10431283	0.87[EUR][1000 genomes]
rs1055876	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10844179	0.82[EUR][1000 genomes]
rs10844183	0.88[EUR][1000 genomes]
rs10844184	0.87[EUR][1000 genomes]
rs10844188	0.91[EUR][1000 genomes]
rs11051925	0.87[EUR][1000 genomes]
rs11051928	0.87[EUR][1000 genomes]
rs11051929	0.87[EUR][1000 genomes]
rs11051932	0.85[EUR][1000 genomes]
rs11051934	0.86[EUR][1000 genomes]
rs11051935	0.87[EUR][1000 genomes]
rs11051936	0.88[EUR][1000 genomes]
rs11051937	0.88[EUR][1000 genomes]
rs11051938	0.91[EUR][1000 genomes]
rs11051939	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs11051940	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11051941	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs11051942	0.91[EUR][1000 genomes]
rs11051943	0.91[EUR][1000 genomes]
rs11051944	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs11051945	0.96[EUR][1000 genomes]
rs11051946	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11536026	0.87[EUR][1000 genomes]
rs11833592	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12229856	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12578899	0.91[EUR][1000 genomes]
rs16919727	0.91[EUR][1000 genomes]
rs16919774	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs1972033	0.80[EUR][1000 genomes]
rs1972438	0.87[EUR][1000 genomes]
rs2036304	0.90[EUR][1000 genomes]
rs2291420	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs2291421	0.91[EUR][1000 genomes]
rs2388988	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2388989	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2728698	0.81[EUR][1000 genomes]
rs2892655	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3748275	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs3748276	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs3789975	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs3816819	0.91[EUR][1000 genomes]
rs4316592	0.91[EUR][1000 genomes]
rs4474533	0.83[EUR][1000 genomes]
rs4604975	0.96[EUR][1000 genomes]
rs4931012	0.90[EUR][1000 genomes]
rs4931621	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs58236386	0.87[EUR][1000 genomes]
rs58926489	0.87[EUR][1000 genomes]
rs58959894	0.95[EUR][1000 genomes]
rs60221824	0.86[EUR][1000 genomes]
rs6488044	0.93[EUR][1000 genomes]
rs7300646	0.94[EUR][1000 genomes]
rs7956708	0.87[EUR][1000 genomes]
rs7962680	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963887	0.87[EUR][1000 genomes]
rs7974653	0.89[EUR][1000 genomes]
rs7977938	0.87[EUR][1000 genomes]
rs950082	0.81[CEU][hapmap]

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
rs2270786	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32457200-32494400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:32460400-32514600	Weak transcription	HMEC	breast
3	chr12:32472800-32493600	Weak transcription	Adipose Nuclei	Adipose
4	chr12:32475400-32500200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:32475600-32532400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:32475800-32492000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:32475800-32495800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:32475800-32502200	Weak transcription	Brain Substantia Nigra	brain
9	chr12:32475800-32512200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:32476400-32505600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:32476400-32515400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:32476600-32493400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:32477200-32500800	Weak transcription	Hela-S3	cervix
14	chr12:32478800-32498800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:32479000-32493600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:32479200-32492400	Weak transcription	Small Intestine	intestine
17	chr12:32479200-32502200	Weak transcription	NHDF-Ad	bronchial
18	chr12:32479200-32504200	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:32479400-32494400	Weak transcription	Right Ventricle	heart
20	chr12:32479400-32501200	Weak transcription	Fetal Brain Male	brain
21	chr12:32479600-32491800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:32480200-32494000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:32480600-32524800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:32481200-32493800	Weak transcription	Fetal Thymus	thymus
25	chr12:32481400-32511800	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:32481600-32496600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:32481600-32497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:32481600-32501800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:32481800-32490800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:32481800-32495800	Weak transcription	Left Ventricle	heart
31	chr12:32482000-32490800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:32482000-32491800	Weak transcription	Fetal Stomach	stomach
33	chr12:32482000-32496000	Weak transcription	HSMM	muscle
34	chr12:32484400-32515600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:32484800-32491800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:32484800-32493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:32484800-32496200	Weak transcription	A549	lung
38	chr12:32485600-32492400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:32485800-32520000	Weak transcription	Fetal Kidney	kidney
40	chr12:32486000-32510800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:32486200-32494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:32486800-32496400	Weak transcription	HUVEC	blood vessel
43	chr12:32487000-32492000	Weak transcription	Pancreas	Pancrea
44	chr12:32487200-32492800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:32487200-32502400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:32487400-32492200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:32487400-32492400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:32487800-32494000	Weak transcription	GM12878-XiMat	blood
49	chr12:32488600-32492000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:32488800-32494200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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