Variant report

Variant	rs11623147
Chromosome Location	chr14:71277713-71277714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr14:71274656-71277729	HEK293-T-REx	kidney:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:71076190..71078982-chr14:71275139..71277878,2	MCF-7	breast:
2	chr14:71102508..71105172-chr14:71277207..71278775,2	MCF-7	breast:
3	chr14:71106760..71110006-chr14:71274602..71279359,4	MCF-7	breast:
4	chr14:70233111..70234704-chr14:71276587..71278198,2	MCF-7	breast:
5	chr14:71218602..71225147-chr14:71276029..71280278,8	MCF-7	breast:
6	chr14:71275321..71276832-chr14:71277641..71279506,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAP3K9	TF binding region
ENSG00000240837	Chromatin interaction
ENSG00000006432	Chromatin interaction
ENSG00000259115	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000245466	Chromatin interaction
ENSG00000133985	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10146964	0.90[CHB][hapmap]
rs11158881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11621236	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11622104	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs11622788	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11622989	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11844844	0.81[ASN][1000 genomes]
rs12437113	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12437247	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12880887	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs12897139	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108537	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108548	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs17108555	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1859464	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34509410	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34548271	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829955	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs67164415	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71425385	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7144786	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs7153601	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs731571	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8014624	0.86[CHB][hapmap]
rs8019156	0.81[CHB][hapmap]

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	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
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11623147	SLC8A3	cis	cerebellum	SCAN
rs11623147	ACOT4	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71273000-71280600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:71274200-71278800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:71274200-71279400	Active TSS	HMEC	breast
4	chr14:71274400-71277800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr14:71274400-71277800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr14:71274400-71278200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr14:71274600-71277800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:71274600-71277800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:71274600-71279400	Active TSS	Esophagus	oesophagus
10	chr14:71274800-71277800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:71274800-71277800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71274800-71278200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr14:71274800-71278600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr14:71274800-71279400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr14:71275000-71277800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr14:71275000-71277800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:71275000-71277800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr14:71275000-71277800	Active TSS	A549	lung
19	chr14:71275200-71277800	Active TSS	Fetal Kidney	kidney
20	chr14:71275200-71278000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr14:71276000-71278600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr14:71276800-71278000	Flanking Active TSS	Fetal Brain Female	brain
23	chr14:71277200-71277800	Flanking Active TSS	Fetal Brain Male	brain
24	chr14:71277200-71277800	Enhancers	Fetal Thymus	thymus
25	chr14:71277200-71278000	Enhancers	Brain Hippocampus Middle	brain
26	chr14:71277200-71278200	Flanking Active TSS	GM12878-XiMat	blood
27	chr14:71277200-71278400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:71277200-71278400	Enhancers	Placenta	Placenta
29	chr14:71277200-71278400	Weak transcription	Lung	lung
30	chr14:71277200-71279200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:71277200-71279200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:71277200-71288000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:71277200-71288400	Weak transcription	Pancreas	Pancrea
34	chr14:71277400-71277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr14:71277400-71277800	Enhancers	Brain Cingulate Gyrus	brain
36	chr14:71277400-71277800	Enhancers	K562	blood
37	chr14:71277400-71278000	Enhancers	Hela-S3	cervix
38	chr14:71277400-71278200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:71277400-71278200	Enhancers	Dnd41	blood
40	chr14:71277400-71278400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:71277400-71279400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr14:71277400-71280600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:71277400-71283800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:71277600-71277800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr14:71277600-71277800	Enhancers	Small Intestine	intestine
46	chr14:71277600-71278000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:71277600-71278000	Enhancers	Brain Anterior Caudate	brain
48	chr14:71277600-71278200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr14:71277600-71278400	Flanking Active TSS	HepG2	liver
50	chr14:71277600-71278600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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