Variant report

Variant	rs16934110
Chromosome Location	chr12:29436743-29436744
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29436726..29437705-chr8:43092410..43092910,2	MCF-7	breast:
2	chr12:29435723..29438704-chr8:43094408..43095931,2	K562	blood:
3	chr12:29436722..29437227-chr8:43092930..43093430,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10161532	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10492378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11050164	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11050165	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11050166	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11050172	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050211	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12298758	1.00[CHB][hapmap]
rs12301257	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12301468	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12304675	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12305672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12308214	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12314513	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12315111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12316548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12319953	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12320036	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap]
rs12321184	1.00[JPT][hapmap]
rs12322493	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16934299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28559992	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3816113	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4931176	0.86[ASW][hapmap];0.91[LWK][hapmap];0.94[YRI][hapmap]
rs7312068	0.86[ASW][hapmap];0.91[LWK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs766764	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16934110	CCBE1	trans	brain	seeQTL
rs16934110	AGMAT	trans	brain	seeQTL
rs16934110	DHRS9	trans	brain	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
3	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
9	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
11	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:29432200-29442800	Weak transcription	Psoas Muscle	Psoas
14	chr12:29432400-29438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:29432800-29445800	Weak transcription	Primary B cells from cord blood	blood
16	chr12:29434200-29449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:29434400-29439000	Enhancers	Osteobl	bone
18	chr12:29435400-29436800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:29435400-29436800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:29435400-29439000	Weak transcription	HSMMtube	muscle
21	chr12:29435400-29439600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:29435800-29439000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:29436000-29437800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:29436000-29440800	Weak transcription	HSMM	muscle
26	chr12:29436400-29438800	Enhancers	NHDF-Ad	bronchial
27	chr12:29436400-29443200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:29436600-29437200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:29436600-29437400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:29436600-29437600	Enhancers	NH-A	brain

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