Variant report

Variant	rs3742878
Chromosome Location	chr14:68087820-68087821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:68085519-68088093	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr14:68086319-68087970	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr14:68085868-68088060	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr14:68085375-68088227	H1-neurons	neurons:	n/a	chr14:68086528-68086538 chr14:68086499-68086512

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68085513..68087982-chr14:68140363..68143281,3	MCF-7	breast:
2	chr14:68081591..68084164-chr14:68086995..68089181,2	K562	blood:
3	chr14:68087492..68090033-chr14:68140902..68143299,2	K562	blood:
4	chr14:68087309..68089150-chr14:68130477..68132954,2	K562	blood:
5	chr14:68087429..68090959-chr14:68140902..68143927,4	K562	blood:
6	chr14:68083940..68088003-chr14:68160289..68162917,5	K562	blood:
7	chr14:68087557..68089288-chr14:68096607..68098723,2	K562	blood:
8	chr14:68065533..68067898-chr14:68086654..68089518,2	K562	blood:
9	chr14:68086481..68089265-chr14:68117411..68120883,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000201529	TF binding region
ENSG00000259648	Chromatin interaction
ENSG00000072042	Chromatin interaction
ENSG00000100568	Chromatin interaction
ENSG00000100564	Chromatin interaction
ENSG00000201529	Chromatin interaction
ENSG00000258626	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11628590	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628666	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433361	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343243	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17249437	0.87[CEU][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17836809	0.93[CEU][hapmap]
rs1885042	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759757	0.93[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759759	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902501	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902503	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573787	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573788	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517376	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67778250	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7144243	0.93[CEU][hapmap]
rs7151920	0.93[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161243	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8012815	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8013117	0.93[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014035	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014048	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3742878	RDH11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68086000-68088000	Active TSS	Psoas Muscle	Psoas
2	chr14:68086000-68088000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr14:68086400-68088000	Active TSS	Brain Angular Gyrus	brain
4	chr14:68087000-68088000	Flanking Active TSS	NHEK	skin
5	chr14:68087200-68088000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:68087200-68088000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr14:68087200-68089200	Weak transcription	HSMMtube	muscle
8	chr14:68087200-68109600	Weak transcription	Gastric	stomach
9	chr14:68087200-68112400	Weak transcription	Aorta	Aorta
10	chr14:68087400-68088000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr14:68087400-68088000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr14:68087400-68088000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr14:68087400-68088000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:68087400-68088000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:68087400-68088000	Flanking Active TSS	Fetal Brain Male	brain
16	chr14:68087400-68088200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:68087400-68088200	Enhancers	NHDF-Ad	bronchial
18	chr14:68087400-68089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:68087400-68089000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr14:68087400-68089000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:68087400-68089400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:68087400-68089400	Weak transcription	HSMM	muscle
23	chr14:68087600-68088000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:68087600-68088000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:68087600-68088000	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr14:68087600-68088000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr14:68087600-68088000	Enhancers	HMEC	breast
28	chr14:68087600-68088000	Enhancers	NH-A	brain
29	chr14:68087600-68088200	Flanking Active TSS	Fetal Brain Female	brain
30	chr14:68087600-68088200	Enhancers	HUVEC	blood vessel
31	chr14:68087600-68088800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr14:68087600-68088800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:68087600-68088800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:68087600-68089000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr14:68087600-68089000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr14:68087600-68089000	Weak transcription	Brain Substantia Nigra	brain
37	chr14:68087600-68089000	Weak transcription	Colon Smooth Muscle	Colon
38	chr14:68087600-68089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr14:68087600-68089200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr14:68087600-68089200	Weak transcription	Adipose Nuclei	Adipose
41	chr14:68087600-68089200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:68087600-68089200	Weak transcription	NHLF	lung
43	chr14:68087600-68089400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:68087600-68089400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr14:68087600-68089400	Weak transcription	Placenta	Placenta
46	chr14:68087600-68089400	Weak transcription	Small Intestine	intestine
47	chr14:68087600-68089400	Weak transcription	Spleen	Spleen
48	chr14:68087600-68089600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:68087600-68089800	Weak transcription	Left Ventricle	heart
50	chr14:68087600-68091600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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