Variant report

Variant	rs13085694
Chromosome Location	chr3:20023990-20023991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19988550..19992168-chr3:20020469..20024167,3	K562	blood:
2	chr3:20022682..20025378-chr3:20026127..20028940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11718997	0.85[ASN][1000 genomes]
rs12714980	0.91[ASN][1000 genomes]
rs13085450	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2127956	0.91[ASN][1000 genomes]
rs2364515	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2929343	0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2929415	0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2948108	0.81[ASN][1000 genomes]
rs2948110	0.82[ASN][1000 genomes]
rs2948111	0.82[ASN][1000 genomes]
rs4858626	0.93[ASN][1000 genomes]
rs4858652	0.88[ASN][1000 genomes]
rs6550237	0.88[ASN][1000 genomes]
rs6550239	0.88[ASN][1000 genomes]
rs6773437	0.87[ASN][1000 genomes]
rs6797890	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613136	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7616422	0.94[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs7627200	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9840653	0.91[ASN][1000 genomes]
rs9858341	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9968079	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS 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	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13085694	EFHB	cis	cerebellum	SCAN
rs13085694	EFHB	cis	parietal	SCAN
rs13085694	CDCA4	trans	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19999600-20027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
3	chr3:20011800-20026400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:20011800-20027400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:20011800-20028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:20012000-20027800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr3:20012000-20027800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:20012200-20025600	Weak transcription	Pancreas	Pancrea
9	chr3:20012200-20026400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:20012400-20025600	Weak transcription	Stomach Mucosa	stomach
11	chr3:20012400-20027600	Strong transcription	Primary B cells from cord blood	blood
12	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
13	chr3:20014400-20025600	Strong transcription	K562	blood
14	chr3:20014400-20027000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:20014600-20026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:20014600-20027600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:20015200-20025200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:20015200-20026800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:20015200-20027000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:20015200-20027200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:20015200-20027600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:20015200-20027600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:20015200-20030000	Strong transcription	Fetal Thymus	thymus
24	chr3:20015400-20025000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:20015400-20025200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:20015400-20025400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:20015400-20025400	Strong transcription	GM12878-XiMat	blood
28	chr3:20015400-20025800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:20015400-20027200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr3:20015400-20027400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:20015400-20027600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:20015400-20028200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:20015400-20028200	Strong transcription	Placenta	Placenta
34	chr3:20015600-20024400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:20015600-20025400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr3:20015600-20025400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:20015600-20025600	Strong transcription	Fetal Lung	lung
38	chr3:20015600-20025800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:20015600-20026200	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:20015600-20026400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:20015600-20026600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:20015600-20026600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:20015600-20026800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:20015600-20027200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:20015600-20027200	Strong transcription	Fetal Intestine Large	intestine
46	chr3:20015600-20027600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:20015800-20024200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:20015800-20025400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:20015800-20025800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:20015800-20026200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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