Variant report

Variant	rs11625397
Chromosome Location	chr14:104027557-104027558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr14:104027540-104028133	H1-hESC	embryonic stem cell:	n/a	n/a
2	HCFC1	chr14:104027237-104030166	Hela-S3	cervix:	n/a	n/a
3	SIN3AK20	chr14:104027394-104030066	MCF-7	breast:	n/a	n/a
4	FOSL2	chr14:104027539-104028006	MCF-7	breast:	n/a	chr14:104027897-104027906
5	EP300	chr14:104027440-104028566	ECC-1	luminal epithelium:	n/a	n/a
6	FOS	chr14:104027545-104027933	MCF10A-Er-Src	breast:	n/a	chr14:104027897-104027906
7	ZNF263	chr14:104027545-104029148	HEK293-T-REx	kidney:	n/a	chr14:104028713-104028722 chr14:104028399-104028408
8	EGR1	chr14:104027429-104028040	MCF-7	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
2	chr14:104016689..104020988-chr14:104027518..104030448,6	MCF-7	breast:
3	chr14:103983696..103988397-chr14:104026059..104029809,6	K562	blood:
4	chr14:104026026..104030833-chr14:104180410..104184978,6	MCF-7	breast:
5	chr14:104014533..104016298-chr14:104025800..104028102,2	K562	blood:
6	chr14:103799415..103801924-chr14:104027086..104029565,3	MCF-7	breast:
7	chr14:104018005..104022715-chr14:104023184..104028959,7	K562	blood:
8	chr14:104026574..104032100-chr14:104033737..104038565,9	MCF-7	breast:
9	chr14:103985364..103989946-chr14:104026445..104030227,8	MCF-7	breast:
10	chr14:104009722..104012574-chr14:104026131..104028003,2	K562	blood:
11	chr14:104003474..104006501-chr14:104024765..104028078,3	MCF-7	breast:
12	chr14:104027061..104029959-chr14:104033088..104037337,3	K562	blood:
13	chr14:104027275..104029645-chr9:131939860..131941591,2	MCF-7	breast:
14	chr14:103992298..103994293-chr14:104026567..104028145,2	K562	blood:
15	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:

No data

Variant related genes	Relation type
KLC1	TF binding region
APOPT1	TF binding region
ENSG00000256500	TF binding region
ENSG00000126215	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000256053	Chromatin interaction
ENSG00000100664	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000188483	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000201184	Chromatin interaction
ENSG00000258851	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11160756	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs11850979	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs12589494	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12897511	0.82[ASN][1000 genomes]
rs2296483	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742465	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs3759586	0.87[JPT][hapmap]
rs4318144	0.81[ASN][1000 genomes]
rs4900589	0.87[JPT][hapmap]
rs57202218	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58601596	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7142016	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155511	0.81[ASN][1000 genomes]
rs729437	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs745079	0.81[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs752624	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8003289	0.87[JPT][hapmap]
rs8007489	0.87[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008382	0.83[AMR][1000 genomes]
rs8008451	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs8021368	0.81[JPT][hapmap]
rs861537	0.87[MEX][hapmap]
rs861544	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs861545	0.82[JPT][hapmap]
rs861547	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs8702	0.86[JPT][hapmap]
rs942862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9652403	0.91[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS 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	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS 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	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902303	chr14:103979953-104034746	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	esv1839595	chr14:103987140-104034746	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv976818	chr14:104023424-104029394	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv827069	chr14:104027502-104028019	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
14	nsv827070	chr14:104027510-104028019	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11625397	CCDC85C	cis	cerebellum	SCAN
rs11625397	C14orf172	cis	multi-tissue	Pritchard
rs11625397	ENSG00000166170	cis	multi-tissue	Pritchard
rs11625397	BAG5	cis	cerebellum	SCAN
rs11625397	MARK3	cis	multi-tissue	Pritchard
rs11625397	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104011400-104027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104013600-104027600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:104019200-104027600	Weak transcription	Colonic Mucosa	Colon
4	chr14:104019800-104027600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:104023200-104027600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr14:104023600-104027600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:104025200-104027600	Weak transcription	Ovary	ovary
8	chr14:104025400-104027800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:104026000-104027600	Genic enhancers	Fetal Muscle Leg	muscle
10	chr14:104026000-104027600	Genic enhancers	Left Ventricle	heart
11	chr14:104026200-104027600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr14:104026200-104027600	Enhancers	Colon Smooth Muscle	Colon
13	chr14:104026200-104027600	Enhancers	Right Atrium	heart
14	chr14:104026400-104027600	Genic enhancers	Fetal Stomach	stomach
15	chr14:104026400-104027800	Enhancers	Fetal Brain Male	brain
16	chr14:104026800-104027600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:104026800-104027600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr14:104026800-104027600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr14:104026800-104028000	Enhancers	Spleen	Spleen
20	chr14:104027000-104027600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:104027000-104027600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:104027000-104027600	Enhancers	Primary T cells from cord blood	blood
23	chr14:104027000-104027600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr14:104027000-104027600	Enhancers	Brain Hippocampus Middle	brain
25	chr14:104027000-104027600	Enhancers	Brain Substantia Nigra	brain
26	chr14:104027000-104027600	Weak transcription	Esophagus	oesophagus
27	chr14:104027000-104027600	Enhancers	Placenta	Placenta
28	chr14:104027000-104027600	Weak transcription	Gastric	stomach
29	chr14:104027000-104027600	Weak transcription	Lung	lung
30	chr14:104027000-104027600	Weak transcription	Pancreas	Pancrea
31	chr14:104027000-104027600	Enhancers	Right Ventricle	heart
32	chr14:104027000-104027600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr14:104027000-104027800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr14:104027000-104027800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr14:104027000-104027800	Genic enhancers	Primary B cells from cord blood	blood
36	chr14:104027000-104027800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:104027000-104028000	Enhancers	Primary B cells from peripheral blood	blood
38	chr14:104027000-104028400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr14:104027000-104028400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr14:104027000-104028400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr14:104027000-104028600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr14:104027200-104027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:104027200-104027600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:104027200-104027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr14:104027200-104027600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr14:104027200-104027600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr14:104027200-104027600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr14:104027200-104027600	Enhancers	Fetal Kidney	kidney
49	chr14:104027200-104027600	Genic enhancers	Fetal Thymus	thymus
50	chr14:104027200-104027600	Enhancers	Small Intestine	intestine

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