Variant report

Variant	rs2651374
Chromosome Location	chr12:32582858-32582859
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	chr12:32580165..32582932-chr12:32583223..32584880,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1045751	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771942	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs10844197	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10844198	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1128591	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12367488	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1500874	0.86[JPT][hapmap]
rs167806	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs186568	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs188978	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs188979	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2062600	0.81[JPT][hapmap]
rs2253237	0.85[EUR][1000 genomes]
rs2253247	0.86[EUR][1000 genomes]
rs2450506	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2455004	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2455005	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2632326	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2632330	0.86[EUR][1000 genomes]
rs2632337	0.86[EUR][1000 genomes]
rs2632363	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2651360	0.86[JPT][hapmap]
rs2651362	0.85[JPT][hapmap]
rs2651363	0.86[JPT][hapmap]
rs2651365	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2651366	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2651367	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2651368	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2651372	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2651375	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2651376	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2651377	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2651380	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2728671	0.86[JPT][hapmap]
rs2728674	0.86[JPT][hapmap]
rs2728678	0.81[JPT][hapmap]
rs2728681	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2728690	0.82[EUR][1000 genomes]
rs2728715	0.80[JPT][hapmap]
rs2733694	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733696	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733703	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2733704	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2733705	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2931554	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs325418	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325419	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325420	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs325421	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325424	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs325425	0.81[CEU][hapmap]
rs4931624	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7297833	0.80[JPT][hapmap]
rs7298319	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs7298381	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs7312698	0.88[EUR][1000 genomes]
rs7315762	0.85[EUR][1000 genomes]
rs950079	0.86[JPT][hapmap]
rs950080	0.86[JPT][hapmap]
rs950081	0.86[JPT][hapmap]
rs950082	0.86[JPT][hapmap]

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
rs2651374	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr12:32573400-32583600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:32573400-32587000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:32573400-32593400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:32574800-32587200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:32575600-32583800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:32576200-32588800	Weak transcription	NHEK	skin
8	chr12:32576200-32589000	Weak transcription	HMEC	breast
9	chr12:32576200-32589200	Weak transcription	Stomach Mucosa	stomach
10	chr12:32580400-32593200	Weak transcription	Fetal Intestine Large	intestine
11	chr12:32580600-32583000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:32581600-32583400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:32581600-32583400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:32582200-32583000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:32582200-32583000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
16	chr12:32582200-32587400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:32582400-32583000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:32582400-32583200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:32582600-32583000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:32582600-32583000	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:32582600-32583000	Weak transcription	Small Intestine	intestine
22	chr12:32582600-32587000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:32582600-32589200	Weak transcription	Ovary	ovary
24	chr12:32582600-32589400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:32582600-32591000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:32582600-32593600	Weak transcription	Fetal Stomach	stomach
27	chr12:32582600-32598600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:32582800-32584000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:32582800-32584200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:32582800-32587200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:32582800-32590200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:32582800-32590400	Weak transcription	Fetal Intestine Small	intestine

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