Variant report

Variant	rs11624118
Chromosome Location	chr14:78138300-78138301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78137716..78140274-chr14:78142246..78143787,2	MCF-7	breast:
2	chr14:78136536..78139253-chr14:78155471..78158284,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLIRP-2	chr14:78137913-78138440	NONHSAT037998

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.90[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10134425	0.85[ASN][1000 genomes]
rs10138747	0.81[ASN][1000 genomes]
rs10139492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10143294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10144448	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10146255	0.81[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs114763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11621719	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11622761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11624103	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11628838	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11628888	0.85[CHB][hapmap]
rs12879880	0.83[ASN][1000 genomes]
rs12885306	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs12887313	0.81[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.83[ASN][1000 genomes]
rs1477264	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.81[ASN][1000 genomes]
rs176948	0.86[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.86[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs176959	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs176961	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176963	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs176965	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs176968	0.85[ASN][1000 genomes]
rs176969	0.85[ASN][1000 genomes]
rs176970	0.85[ASN][1000 genomes]
rs176972	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs176975	0.85[ASN][1000 genomes]
rs176976	0.85[ASN][1000 genomes]
rs176977	0.81[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2111831	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2267763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2284233	0.83[ASN][1000 genomes]
rs2284234	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2284235	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs3783981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3783982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4632066	0.90[CHB][hapmap]
rs4641655	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4899673	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs4899674	0.84[ASN][1000 genomes]
rs4903627	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4903638	0.83[ASN][1000 genomes]
rs61992863	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61992864	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61992867	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61992868	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6574392	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574394	0.85[ASN][1000 genomes]
rs6574399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7141469	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7142262	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7142390	0.90[CHB][hapmap]
rs7143075	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7143926	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7145717	0.83[ASN][1000 genomes]
rs7148078	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7148126	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7150531	0.82[ASN][1000 genomes]
rs7151685	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7159821	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159992	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160003	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160355	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs717682	0.83[ASN][1000 genomes]
rs759713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.85[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.84[ASN][1000 genomes]
rs9323649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9788619	0.84[AMR][1000 genomes]

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	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
8	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
9	nsv9156	chr14:78138141-78140714	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11624118	RPS6KL1	cis	cerebellum	SCAN
rs11624118	PAPLN	cis	parietal	SCAN
rs11624118	ALDH6A1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78121400-78139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:78121800-78139800	Weak transcription	Gastric	stomach
3	chr14:78122000-78139600	Weak transcription	Fetal Intestine Large	intestine
4	chr14:78122000-78139800	Weak transcription	Pancreas	Pancrea
5	chr14:78123400-78138800	Weak transcription	Liver	Liver
6	chr14:78123800-78139000	Weak transcription	Left Ventricle	heart
7	chr14:78125400-78139800	Weak transcription	Right Ventricle	heart
8	chr14:78126800-78138800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:78126800-78139000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:78126800-78139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:78126800-78139800	Weak transcription	Spleen	Spleen
12	chr14:78127400-78138800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:78127400-78139800	Weak transcription	Lung	lung
14	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:78127600-78138600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:78127600-78138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr14:78127600-78138800	Weak transcription	Brain Anterior Caudate	brain
18	chr14:78127600-78139000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr14:78127600-78139200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:78127600-78139200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:78127600-78139800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:78127600-78140000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:78127600-78140000	Weak transcription	Esophagus	oesophagus
24	chr14:78127800-78138600	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:78127800-78139600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr14:78127800-78139800	Weak transcription	Brain Germinal Matrix	brain
27	chr14:78128000-78138600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:78128000-78138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr14:78128000-78139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr14:78128000-78157800	Weak transcription	Fetal Brain Male	brain
31	chr14:78128200-78139600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:78128800-78138800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr14:78129000-78138800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:78129000-78138800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:78129000-78139800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:78129200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr14:78129800-78147600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr14:78130000-78138800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:78130000-78138800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:78130000-78139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr14:78130200-78139400	Weak transcription	HUVEC	blood vessel
42	chr14:78130200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr14:78130400-78139200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr14:78130400-78139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:78130400-78139400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr14:78130400-78139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:78130400-78139800	Weak transcription	Hela-S3	cervix
48	chr14:78130400-78139800	Weak transcription	NHEK	skin
49	chr14:78130400-78140200	Weak transcription	HMEC	breast
50	chr14:78130600-78139200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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