Variant report

Variant	rs2651380
Chromosome Location	chr12:32577181-32577182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1045751	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10844197	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10844198	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128591	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12367488	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs167806	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs186568	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs188978	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs188979	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2062601	0.81[AMR][1000 genomes]
rs2253237	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253247	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2450506	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2455004	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2455005	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2632326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2632330	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2632337	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2632363	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2651365	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2651366	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2651367	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2651368	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2651372	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2651374	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2651375	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2651376	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2651377	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2728681	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2728690	0.81[EUR][1000 genomes]
rs2733694	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733696	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733703	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733704	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733705	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2931554	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325418	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325419	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325420	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325421	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325423	0.80[AMR][1000 genomes]
rs325424	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4931624	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7312698	0.87[EUR][1000 genomes]
rs7315762	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7315797	0.80[AMR][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
rs2651380	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 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	chr12:32573000-32577600	Weak transcription	Fetal Intestine Small	intestine
3	chr12:32573000-32582200	Weak transcription	Ovary	ovary
4	chr12:32573400-32582000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:32573400-32582400	Weak transcription	Pancreas	Pancrea
6	chr12:32573400-32583600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:32573400-32587000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:32573400-32593400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:32574600-32578000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:32574600-32578400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:32574800-32578400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:32574800-32579400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:32574800-32587200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:32575600-32583800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:32575800-32577400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:32575800-32577600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:32576000-32582200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:32576200-32582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:32576200-32588800	Weak transcription	NHEK	skin
20	chr12:32576200-32589000	Weak transcription	HMEC	breast
21	chr12:32576200-32589200	Weak transcription	Stomach Mucosa	stomach
22	chr12:32576600-32577600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:32576800-32579400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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