Variant report

Variant	rs7159558
Chromosome Location	chr14:77742929-77742930
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	chr14:77742580..77744356-chr14:77768244..77771004,2	MCF-7	breast:
3	chr14:77741661..77744211-chr14:77747237..77749936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10138030	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1055592	0.86[CHD][hapmap]
rs11159254	1.00[ASN][1000 genomes]
rs11547793	0.95[CHD][hapmap];0.90[JPT][hapmap]
rs11547794	1.00[ASN][1000 genomes]
rs11624564	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11627257	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1600005	0.89[ASN][1000 genomes]
rs17105672	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2042045	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2111699	0.86[CHB][hapmap]
rs2193594	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2216089	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270421	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2287387	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs2287388	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs2287392	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs2287395	0.80[CHB][hapmap]
rs2363641	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2363643	0.86[CHB][hapmap]
rs3783986	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs3783988	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs3783989	0.90[JPT][hapmap]
rs3815626	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4147578	0.87[CHB][hapmap]
rs4899650	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4903565	1.00[ASN][1000 genomes]
rs4903567	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs59730492	0.83[ASN][1000 genomes]
rs61990261	0.85[ASN][1000 genomes]
rs6574367	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7142812	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7158951	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009261	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009733	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8016187	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1361	chr14:77707417-77753024	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7159558	LIN52	cis	parietal	SCAN
rs7159558	PAPLN	cis	parietal	SCAN
rs7159558	NRXN3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77737400-77743000	Weak transcription	Dnd41	blood
2	chr14:77738800-77743400	Weak transcription	A549	lung
3	chr14:77738800-77749600	Weak transcription	NHDF-Ad	bronchial
4	chr14:77739000-77749800	Weak transcription	HUVEC	blood vessel
5	chr14:77739200-77743600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr14:77739400-77744600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:77739400-77745400	Weak transcription	Fetal Lung	lung
8	chr14:77739400-77749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:77739600-77744400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr14:77739600-77745400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:77739600-77745600	Weak transcription	Primary B cells from cord blood	blood
12	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:77739800-77743400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr14:77739800-77743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:77739800-77743800	Weak transcription	HSMMtube	muscle
16	chr14:77740000-77744600	Weak transcription	Colonic Mucosa	Colon
17	chr14:77740000-77744600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr14:77740000-77749600	Weak transcription	HMEC	breast
19	chr14:77740200-77746400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:77740200-77749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr14:77740200-77750800	Weak transcription	Fetal Thymus	thymus
22	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
24	chr14:77740400-77743000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:77740400-77743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:77740400-77746200	Weak transcription	NHEK	skin
27	chr14:77740400-77749200	Weak transcription	Osteobl	bone
28	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
29	chr14:77740600-77743400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr14:77740600-77743600	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:77740600-77743600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr14:77740600-77744400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:77740600-77744400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr14:77740800-77743400	Weak transcription	Left Ventricle	heart
35	chr14:77740800-77743400	Weak transcription	NHLF	lung
36	chr14:77740800-77758000	Strong transcription	Fetal Stomach	stomach
37	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:77741000-77743200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:77741000-77749600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr14:77741000-77750000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr14:77741000-77750400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr14:77741200-77745200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:77741200-77749400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:77741400-77753600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr14:77741600-77743000	Enhancers	Fetal Brain Male	brain
47	chr14:77741600-77743000	Genic enhancers	Fetal Brain Female	brain
48	chr14:77741600-77744400	Weak transcription	HepG2	liver
49	chr14:77741800-77746600	Strong transcription	Brain Germinal Matrix	brain
50	chr14:77741800-77749000	Strong transcription	Fetal Intestine Small	intestine

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