Variant report

Variant	rs12886631
Chromosome Location	chr14:78172675-78172676
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78170877..78172859-chr14:78173007..78174927,2	K562	blood:
2	chr14:78169975..78173523-chr14:78173651..78176580,3	MCF-7	breast:
3	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119705	Chromatin interaction
ENSG00000100601	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1008989	0.91[CHB][hapmap]
rs10483885	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1076496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12432030	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12587584	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12587825	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12880300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12880840	0.80[ASN][1000 genomes]
rs12881898	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12885306	0.84[CEU][hapmap]
rs12889788	0.86[CHB][hapmap]
rs12891621	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12892669	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1477264	0.88[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs176947	0.81[EUR][1000 genomes]
rs176977	0.83[EUR][1000 genomes]
rs2267755	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2267757	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2270443	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261431	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35657726	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4540996	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899673	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4899676	0.85[AMR][1000 genomes]
rs4903624	0.88[CEU][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes]
rs4903644	0.80[ASN][1000 genomes]
rs67408612	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145979	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148078	0.84[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs72688831	0.80[ASN][1000 genomes]
rs8003389	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8003715	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12886631	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:78158600-78172800	Weak transcription	NHDF-Ad	bronchial
4	chr14:78163800-78173400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:78163800-78173400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:78163800-78173400	Weak transcription	Right Ventricle	heart
7	chr14:78164000-78173000	Weak transcription	HSMMtube	muscle
8	chr14:78164000-78173400	Weak transcription	Aorta	Aorta
9	chr14:78166400-78172800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:78168000-78172800	Weak transcription	Psoas Muscle	Psoas
11	chr14:78169000-78173000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:78169200-78172800	Weak transcription	HUVEC	blood vessel
13	chr14:78169600-78173400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:78169800-78172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:78169800-78172800	Weak transcription	Brain Germinal Matrix	brain
16	chr14:78170600-78173200	Weak transcription	Colonic Mucosa	Colon
17	chr14:78170800-78172800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:78170800-78173200	Weak transcription	Gastric	stomach
19	chr14:78170800-78173400	Weak transcription	Pancreas	Pancrea
20	chr14:78171000-78172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr14:78171000-78172800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:78171000-78172800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:78171000-78172800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr14:78171000-78172800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:78171000-78172800	Weak transcription	Fetal Brain Male	brain
26	chr14:78171000-78172800	Weak transcription	Fetal Kidney	kidney
27	chr14:78171000-78173400	Weak transcription	Esophagus	oesophagus
28	chr14:78171200-78172800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr14:78171200-78172800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:78171200-78172800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:78171200-78172800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:78171200-78172800	Weak transcription	Primary T cells from cord blood	blood
33	chr14:78171200-78172800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr14:78171200-78172800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr14:78171200-78172800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr14:78171200-78172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:78171200-78172800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr14:78171200-78172800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr14:78171200-78172800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr14:78171200-78172800	Weak transcription	Spleen	Spleen
41	chr14:78171200-78172800	Weak transcription	A549	lung
42	chr14:78171200-78172800	Weak transcription	HSMM	muscle
43	chr14:78171200-78172800	Weak transcription	NH-A	brain
44	chr14:78171200-78172800	Weak transcription	NHLF	lung
45	chr14:78171200-78173200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr14:78171200-78173200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:78171200-78173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr14:78171200-78173400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr14:78171200-78173400	Weak transcription	Lung	lung
50	chr14:78171400-78172800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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