Variant report

Variant	rs11051980
Chromosome Location	chr12:32550172-32550173
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10771944	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10844194	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10844195	0.85[ASN][1000 genomes]
rs10844202	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11051966	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051967	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11052006	0.88[AMR][1000 genomes]
rs12815894	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2087166	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35926650	0.93[ASN][1000 genomes]
rs61927215	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488053	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7299524	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7312869	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7971525	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs883404	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11051980	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32544200-32550800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:32544200-32551600	Weak transcription	Gastric	stomach
3	chr12:32544200-32551800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:32544400-32550600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:32544400-32551800	Weak transcription	Ovary	ovary
6	chr12:32544400-32551800	Weak transcription	HUVEC	blood vessel
7	chr12:32544600-32550800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:32544600-32551200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:32544600-32551600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:32548400-32550200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:32548400-32550600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:32548400-32550800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:32548400-32551600	Weak transcription	A549	lung
14	chr12:32548600-32550400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:32548600-32550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:32548800-32550400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:32548800-32550400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:32549000-32550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:32549200-32550400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:32549200-32550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:32550000-32550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:32550000-32551200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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