Variant report

Variant	rs1684123
Chromosome Location	chr12:32278032-32278033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1144718	0.83[EUR][1000 genomes]
rs1684149	0.82[CEU][hapmap]
rs2683474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv976030	chr12:32153446-32307541	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv898969	chr12:32224948-32375677	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1042317	chr12:32228872-32316774	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1041733	chr12:32247427-32312547	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1684123	C12orf35	cis	parietal	SCAN
rs1684123	H3F3C	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32262400-32287400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:32262400-32290200	Weak transcription	Primary B cells from cord blood	blood
3	chr12:32263200-32287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:32268800-32287200	Weak transcription	Lung	lung
5	chr12:32269000-32285400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:32269000-32286400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:32269000-32286400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:32269000-32287400	Weak transcription	Aorta	Aorta
9	chr12:32269000-32287400	Weak transcription	Spleen	Spleen
10	chr12:32269000-32340200	Weak transcription	Dnd41	blood
11	chr12:32269200-32287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:32269200-32287200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:32269400-32286800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:32269800-32286400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:32270400-32278200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:32270400-32279600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:32270600-32278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:32270600-32285800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:32270600-32287000	Weak transcription	HSMMtube	muscle
20	chr12:32270600-32287000	Weak transcription	HUVEC	blood vessel
21	chr12:32270600-32287200	Weak transcription	NHEK	skin
22	chr12:32272000-32288600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:32272200-32287000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:32272200-32287200	Weak transcription	Left Ventricle	heart
25	chr12:32272400-32280400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:32273600-32278200	Weak transcription	HSMM	muscle
27	chr12:32273600-32279800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:32273600-32292200	Weak transcription	Small Intestine	intestine
29	chr12:32273800-32280400	Weak transcription	Fetal Brain Male	brain
30	chr12:32273800-32280600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:32273800-32285400	Weak transcription	GM12878-XiMat	blood
32	chr12:32273800-32286200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:32273800-32286200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:32273800-32287000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:32274000-32279200	Weak transcription	Hela-S3	cervix
36	chr12:32275000-32278400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32275600-32278200	Enhancers	Fetal Brain Female	brain
38	chr12:32275600-32278800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:32275800-32278400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:32276200-32278400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:32276600-32278600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr12:32277000-32278600	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr12:32277000-32278600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:32277200-32278400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:32277400-32278600	Enhancers	Osteobl	bone
46	chr12:32277600-32278200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr12:32277600-32278200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:32277600-32278200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:32277600-32278200	Enhancers	Ovary	ovary
50	chr12:32277600-32278400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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