Variant report

Variant	rs4903627
Chromosome Location	chr14:78130569-78130570
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78129873..78132369-chr14:78135143..78137756,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10139492	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10143249	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10143294	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10144448	0.80[CHD][hapmap]
rs10873309	0.86[CHD][hapmap]
rs114763	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11621719	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11622761	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11624103	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11624118	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11626349	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs11628838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477264	0.80[CHD][hapmap]
rs176901	0.82[CHD][hapmap]
rs176941	0.83[GIH][hapmap]
rs176959	0.85[GIH][hapmap]
rs176961	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs176965	0.85[GIH][hapmap]
rs2080703	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2111831	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2267750	0.86[CHD][hapmap]
rs2267756	1.00[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2267762	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2267763	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2267764	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2277917	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2284234	0.85[GIH][hapmap]
rs2284235	0.85[GIH][hapmap]
rs2299921	0.86[CHD][hapmap]
rs2299922	0.82[CHD][hapmap]
rs2299924	0.83[CHD][hapmap]
rs2299927	0.82[CHD][hapmap]
rs2299928	0.83[CHD][hapmap]
rs3783981	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3783982	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4641655	0.83[AMR][1000 genomes]
rs4899670	1.00[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4903626	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61992863	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61992864	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61992867	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61992868	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6574392	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7141469	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7142262	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7143075	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7144314	0.82[CHD][hapmap]
rs7148078	0.80[CHD][hapmap]
rs7151685	0.80[CHD][hapmap];0.85[GIH][hapmap]
rs7159821	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7159992	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7160003	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7160355	0.83[AMR][1000 genomes]
rs759713	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8015645	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9323649	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9323651	0.80[CHD][hapmap];0.85[GIH][hapmap]
rs9788619	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944097	0.80[CHD][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	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv9155	chr14:78118162-78133830	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv869872	chr14:78119527-78161340	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv3693172	chr14:78130479-78152921	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4903627	PAPLN	cis	parietal	SCAN
rs4903627	RPS6KL1	cis	cerebellum	SCAN
rs4903627	ALDH6A1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78120600-78138200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr14:78121400-78139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:78121800-78139800	Weak transcription	Gastric	stomach
4	chr14:78122000-78139600	Weak transcription	Fetal Intestine Large	intestine
5	chr14:78122000-78139800	Weak transcription	Pancreas	Pancrea
6	chr14:78123000-78137400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr14:78123400-78138800	Weak transcription	Liver	Liver
8	chr14:78123800-78136600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:78123800-78139000	Weak transcription	Left Ventricle	heart
10	chr14:78125400-78139800	Weak transcription	Right Ventricle	heart
11	chr14:78126600-78138000	Weak transcription	Primary B cells from cord blood	blood
12	chr14:78126800-78138800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:78126800-78139000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:78126800-78139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:78126800-78139800	Weak transcription	Spleen	Spleen
16	chr14:78127400-78138800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr14:78127400-78139800	Weak transcription	Lung	lung
18	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr14:78127600-78137400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr14:78127600-78138600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:78127600-78138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:78127600-78138800	Weak transcription	Brain Anterior Caudate	brain
23	chr14:78127600-78139000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr14:78127600-78139200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:78127600-78139200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:78127600-78139800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:78127600-78140000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:78127600-78140000	Weak transcription	Esophagus	oesophagus
29	chr14:78127800-78138000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:78127800-78138600	Weak transcription	Brain Hippocampus Middle	brain
31	chr14:78127800-78139600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr14:78127800-78139800	Weak transcription	Brain Germinal Matrix	brain
33	chr14:78128000-78132400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr14:78128000-78138000	Weak transcription	Fetal Brain Female	brain
35	chr14:78128000-78138600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:78128000-78138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr14:78128000-78139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr14:78128000-78157800	Weak transcription	Fetal Brain Male	brain
39	chr14:78128200-78139600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:78128600-78130600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr14:78128800-78130600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:78128800-78138800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr14:78129000-78138800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:78129000-78138800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr14:78129000-78139800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:78129200-78132600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr14:78129200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:78129400-78130800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr14:78129800-78147600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr14:78130000-78130600	Enhancers	Adipose Nuclei	Adipose

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