Variant report

Variant	rs3829955
Chromosome Location	chr14:71199452-71199453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10146964	0.90[CHB][hapmap]
rs10148127	0.95[ASN][1000 genomes]
rs11158881	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11621251	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622104	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11622989	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs11623147	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs12435875	0.82[ASN][1000 genomes]
rs12437113	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12880887	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs17108454	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108539	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap]
rs17108548	0.95[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap]
rs1859464	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs6573976	0.81[AMR][1000 genomes]
rs7144786	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7153601	0.83[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs731571	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs8006539	0.80[MEX][hapmap]
rs8014624	0.86[CHB][hapmap]
rs8019156	0.81[CHB][hapmap]

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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3829955	DCAF4	cis	cerebellum	SCAN
rs3829955	ACOT4	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71180800-71200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
3	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
5	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
6	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
8	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
10	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr14:71193800-71209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr14:71194000-71208400	Weak transcription	Brain Substantia Nigra	brain
16	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
17	chr14:71194200-71209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:71194400-71201800	Weak transcription	Right Atrium	heart
19	chr14:71194400-71210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:71194400-71213400	Weak transcription	Psoas Muscle	Psoas
21	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
22	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr14:71195400-71200800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:71195400-71200800	Strong transcription	Primary B cells from cord blood	blood
26	chr14:71195400-71201600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:71195600-71200200	Strong transcription	Pancreas	Pancrea
28	chr14:71195600-71202200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr14:71195600-71209400	Strong transcription	Placenta	Placenta
30	chr14:71195600-71209600	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr14:71195600-71210000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr14:71196000-71200400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:71196000-71200800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:71196200-71201200	Strong transcription	Brain Germinal Matrix	brain
35	chr14:71196200-71209200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr14:71196200-71217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr14:71196400-71200200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:71196400-71201800	Strong transcription	Fetal Stomach	stomach
39	chr14:71196400-71202000	Strong transcription	Fetal Intestine Small	intestine
40	chr14:71196400-71209400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:71196600-71200600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr14:71196600-71200600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:71196600-71201600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr14:71196800-71200400	Weak transcription	GM12878-XiMat	blood
45	chr14:71196800-71206600	Weak transcription	Aorta	Aorta
46	chr14:71197000-71201400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr14:71197200-71200600	Strong transcription	Spleen	Spleen
49	chr14:71197400-71204600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr14:71197600-71200400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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