Variant report

Variant	rs12892669
Chromosome Location	chr14:78173027-78173028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr14:78172988-78176324	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:78169975..78173523-chr14:78173651..78176580,3	MCF-7	breast:
2	chr14:78116603..78122891-chr14:78172785..78176058,7	MCF-7	breast:
3	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:

Variant related genes	Relation type
ALKBH1	TF binding region
SLIRP	TF binding region
ENSG00000100601	Chromatin interaction
ENSG00000258668	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1008989	0.91[CHB][hapmap]
rs1076496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12432030	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587155	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12587584	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587825	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12880300	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs12880840	0.80[ASN][1000 genomes]
rs12881898	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12886631	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12889788	0.86[CHB][hapmap]
rs12891621	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2267755	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267757	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2270443	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299931	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35261431	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35657726	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4540996	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899676	0.83[AMR][1000 genomes]
rs4903624	0.83[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs4903644	0.80[ASN][1000 genomes]
rs67408612	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145979	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72688831	0.80[ASN][1000 genomes]
rs8003389	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8003715	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12892669	SPTLC2	cis	cerebellum	SCAN
rs12892669	ADCK1	cis	lymphoblastoid	seeQTL
rs12892669	RPS6KL1	cis	cerebellum	SCAN
rs12892669	ALKBH1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:78163800-78173400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:78163800-78173400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:78163800-78173400	Weak transcription	Right Ventricle	heart
6	chr14:78164000-78173400	Weak transcription	Aorta	Aorta
7	chr14:78169600-78173400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:78170600-78173200	Weak transcription	Colonic Mucosa	Colon
9	chr14:78170800-78173200	Weak transcription	Gastric	stomach
10	chr14:78170800-78173400	Weak transcription	Pancreas	Pancrea
11	chr14:78171000-78173400	Weak transcription	Esophagus	oesophagus
12	chr14:78171200-78173200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:78171200-78173200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:78171200-78173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:78171200-78173400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:78171200-78173400	Weak transcription	Lung	lung
17	chr14:78171400-78173200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr14:78171400-78173200	Weak transcription	Placenta	Placenta
19	chr14:78171400-78173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:78171600-78173200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr14:78171600-78173400	Weak transcription	Fetal Thymus	thymus
22	chr14:78171800-78173200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr14:78171800-78173400	Weak transcription	Fetal Muscle Leg	muscle
24	chr14:78171800-78173400	Weak transcription	Left Ventricle	heart
25	chr14:78172000-78173200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr14:78172000-78173200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr14:78172000-78173400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr14:78172600-78173200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr14:78172600-78173200	Enhancers	Primary B cells from cord blood	blood
30	chr14:78172600-78173200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr14:78172600-78173200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr14:78172600-78173200	Enhancers	Adipose Nuclei	Adipose
33	chr14:78172600-78173200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr14:78172600-78173200	Enhancers	Fetal Heart	heart
35	chr14:78172600-78173200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr14:78172600-78173200	Flanking Active TSS	HepG2	liver
37	chr14:78172600-78173400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr14:78172600-78173400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr14:78172600-78173400	Enhancers	Small Intestine	intestine
40	chr14:78172600-78173400	Flanking Active TSS	Hela-S3	cervix
41	chr14:78172600-78173600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:78172600-78173600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr14:78172600-78173600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr14:78172600-78173600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr14:78172600-78175800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr14:78172600-78176000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr14:78172800-78173200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:78172800-78173200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr14:78172800-78173200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:78172800-78173200	Enhancers	Brain Substantia Nigra	brain

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