Variant report

Variant	rs4903567
Chromosome Location	chr14:77753970-77753971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77741494..77746628-chr14:77751488..77756217,6	MCF-7	breast:
2	chr14:77752243..77754429-chr14:77756635..77759049,2	MCF-7	breast:
3	chr14:77751328..77755884-chr14:77785355..77788655,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10138030	0.98[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1055592	0.86[CHD][hapmap]
rs11547793	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs11624564	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs11624859	0.89[ASN][1000 genomes]
rs11626281	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11627257	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12431465	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17105672	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2042045	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2098380	0.86[CHB][hapmap]
rs2111699	0.91[CHB][hapmap]
rs2193594	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2216089	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2270421	0.91[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2270423	0.82[CHB][hapmap]
rs2287387	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287388	0.98[CHD][hapmap];0.82[JPT][hapmap]
rs2287392	0.98[CHD][hapmap];0.82[JPT][hapmap]
rs2287395	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2363641	0.95[CHB][hapmap]
rs2363642	0.83[ASN][1000 genomes]
rs2363643	0.91[CHB][hapmap]
rs3783986	0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3783988	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs3783989	0.82[JPT][hapmap]
rs3815626	0.95[CHB][hapmap]
rs4147578	0.89[CHB][hapmap]
rs4899650	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs4903568	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4903569	0.88[ASN][1000 genomes]
rs59630055	0.83[ASN][1000 genomes]
rs61990299	0.89[ASN][1000 genomes]
rs6574367	0.95[CHB][hapmap]
rs67873774	0.89[ASN][1000 genomes]
rs7142812	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7158951	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs7159558	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs7160188	0.83[ASN][1000 genomes]
rs8008449	0.83[ASN][1000 genomes]
rs8009261	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs8009733	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs8016187	0.87[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS 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	107 gene(s)	inside rSNPs	diseases
2	nsv902104	chr14:77720741-77756321	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4903567	LIN52	cis	parietal	SCAN
rs4903567	GSTZ1	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
4	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
5	chr14:77740800-77758000	Strong transcription	Fetal Stomach	stomach
6	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:77741800-77755400	Strong transcription	Fetal Muscle Leg	muscle
9	chr14:77741800-77757200	Strong transcription	Liver	Liver
10	chr14:77741800-77758600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
12	chr14:77742000-77756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:77742000-77757400	Weak transcription	Right Atrium	heart
14	chr14:77742000-77766600	Strong transcription	Placenta	Placenta
15	chr14:77742200-77755000	Strong transcription	Lung	lung
16	chr14:77742200-77757600	Strong transcription	Ovary	ovary
17	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr14:77742400-77755000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:77742400-77755200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr14:77742400-77766400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:77742400-77766400	Strong transcription	Adipose Nuclei	Adipose
22	chr14:77742400-77780200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:77742600-77755000	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:77742600-77756600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr14:77742600-77757400	Strong transcription	Brain Substantia Nigra	brain
28	chr14:77742600-77759400	Strong transcription	Brain Anterior Caudate	brain
29	chr14:77742600-77759600	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr14:77742600-77766600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr14:77742800-77754400	Strong transcription	Aorta	Aorta
32	chr14:77742800-77755400	Strong transcription	Brain Hippocampus Middle	brain
33	chr14:77742800-77755400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:77742800-77757200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr14:77743200-77760400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:77743400-77754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:77743400-77754800	Strong transcription	A549	lung
38	chr14:77743400-77757600	Strong transcription	Left Ventricle	heart
39	chr14:77744000-77771400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr14:77744400-77760200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:77745400-77755200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr14:77746200-77755200	Strong transcription	NHEK	skin
43	chr14:77746600-77767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr14:77746800-77762200	Weak transcription	Colonic Mucosa	Colon
45	chr14:77747200-77762000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:77747600-77756800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr14:77747800-77755200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr14:77748000-77754400	Strong transcription	Fetal Lung	lung
49	chr14:77748200-77755200	Strong transcription	Primary T cells from cord blood	blood
50	chr14:77748200-77757400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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