Variant report

Variant	rs17536892
Chromosome Location	chr14:35760062-35760063
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr14:35759796-35762243	HepG2	liver:	n/a	n/a
2	MYBL2	chr14:35759749-35760581	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:35759856-35762272	HepG2	liver:	n/a	n/a
4	MXI1	chr14:35760019-35760146	HepG2	liver:	n/a	n/a
5	HEY1	chr14:35759901-35760591	HepG2	liver:	n/a	n/a
6	POLR2A	chr14:35759874-35760605	HepG2	liver:	n/a	n/a
7	POLR2A	chr14:35759888-35760348	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:35759775-35762762	HepG2	liver:	n/a	n/a
9	HEY1	chr14:35759838-35762159	HepG2	liver:	n/a	n/a
10	ARID3A	chr14:35759977-35760372	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:35757780..35767592-chr14:35866063..35878024,53	MCF-7	breast:
2	chr14:35701633..35705447-chr14:35760005..35763215,4	MCF-7	breast:
3	chr14:35757192..35766588-chr14:35865950..35877395,53	MCF-7	breast:

No data

Variant related genes	Relation type
PSMA6	TF binding region
ENSG00000265530	TF binding region
ENSG00000100906	Chromatin interaction
ENSG00000256243	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10134120	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10137628	0.94[EUR][1000 genomes]
rs10138507	0.83[EUR][1000 genomes]
rs10141237	0.94[TSI][hapmap]
rs10438061	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs17103097	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs17103098	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs17103110	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17456102	1.00[ASW][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]
rs17457389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17457568	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17458137	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17458214	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17458367	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17458562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17458715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17512725	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17513024	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17535082	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17536948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537213	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597246	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17597267	0.94[TSI][hapmap]
rs17597667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17598437	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17598701	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17598816	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2057336	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2057339	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28446606	0.83[EUR][1000 genomes]
rs28472413	0.83[EUR][1000 genomes]
rs28510695	0.94[EUR][1000 genomes]
rs28549180	0.82[EUR][1000 genomes]
rs45573840	1.00[AFR][1000 genomes]
rs4982256	0.88[EUR][1000 genomes]
rs6571711	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7140912	1.00[CEU][hapmap]
rs7143518	1.00[AFR][1000 genomes]
rs7147426	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7150752	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7151763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7154558	0.87[CEU][hapmap]
rs7156874	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7159008	1.00[CEU][hapmap]
rs8005196	0.87[CEU][hapmap]
rs8014945	1.00[AFR][1000 genomes]
rs8015909	0.90[EUR][1000 genomes]
rs8017330	0.88[TSI][hapmap]
rs8017676	0.94[TSI][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	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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	73 gene(s)	inside rSNPs	diseases
2	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
5	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
6	nsv1038396	chr14:35714499-35788189	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1045288	chr14:35735886-35788189	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1043840	chr14:35739319-35791879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1794822	chr14:35755087-35761366	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17536892	FAM177A1	cis	cerebellum	SCAN
rs17536892	KIAA0391	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35684600-35760800	Weak transcription	HSMM	muscle
2	chr14:35706800-35760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:35716800-35760600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr14:35716800-35761000	Weak transcription	Spleen	Spleen
5	chr14:35717000-35760800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:35722000-35760800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr14:35727200-35761000	Weak transcription	NHLF	lung
8	chr14:35730200-35760600	Weak transcription	Fetal Brain Female	brain
9	chr14:35734400-35760600	Weak transcription	Right Ventricle	heart
10	chr14:35734400-35760800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr14:35736000-35760800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr14:35737400-35761000	Weak transcription	Gastric	stomach
13	chr14:35741200-35760800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr14:35743400-35760800	Weak transcription	HMEC	breast
15	chr14:35743600-35760800	Weak transcription	Brain Anterior Caudate	brain
16	chr14:35743800-35760800	Weak transcription	Osteobl	bone
17	chr14:35744000-35760800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr14:35744000-35760800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:35744000-35760800	Weak transcription	Brain Substantia Nigra	brain
20	chr14:35744000-35760800	Weak transcription	Fetal Lung	lung
21	chr14:35744000-35760800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:35744000-35761000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:35744400-35760800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr14:35744800-35760800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:35745200-35760600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr14:35745200-35760800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:35745400-35760800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:35745600-35760800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:35745800-35760400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:35745800-35760800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr14:35746000-35760800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr14:35746000-35760800	Weak transcription	Brain Hippocampus Middle	brain
33	chr14:35746000-35760800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr14:35746000-35760800	Weak transcription	A549	lung
35	chr14:35746000-35761000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr14:35746200-35760800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr14:35746600-35760800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:35746600-35760800	Weak transcription	Aorta	Aorta
39	chr14:35747200-35761000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:35748000-35760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:35750600-35761000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr14:35751600-35760600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:35752000-35761000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr14:35752400-35760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr14:35752400-35760600	Weak transcription	Fetal Stomach	stomach
46	chr14:35753600-35760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:35754000-35760800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr14:35754400-35760600	Weak transcription	Small Intestine	intestine
49	chr14:35755800-35760800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:35756200-35760800	Enhancers	Fetal Thymus	thymus

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