Variant report

Variant	rs2299931
Chromosome Location	chr14:78163851-78163852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78157152..78158928-chr14:78163519..78165919,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1008989	0.91[CHB][hapmap]
rs10483885	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1076496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12432030	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12587584	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12587825	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12880300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12880840	0.80[ASN][1000 genomes]
rs12881898	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12885306	0.84[CEU][hapmap]
rs12886631	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]
rs12889788	0.86[CHB][hapmap]
rs12891621	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12892669	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1477264	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs176977	0.81[EUR][1000 genomes]
rs2267755	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2267757	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2270443	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35261431	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35657726	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4540996	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899673	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4899676	0.86[AMR][1000 genomes]
rs4903624	0.88[CEU][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes]
rs4903644	0.80[ASN][1000 genomes]
rs67408612	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145979	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148078	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs72688831	0.80[ASN][1000 genomes]
rs8003389	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8003715	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299931	ADCK1	cis	lymphoblastoid	seeQTL
rs2299931	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:78148400-78164400	Weak transcription	Psoas Muscle	Psoas
6	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:78149800-78164200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:78152200-78164200	Strong transcription	Liver	Liver
10	chr14:78152200-78164600	Strong transcription	Adipose Nuclei	Adipose
11	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:78152800-78165400	Strong transcription	Placenta	Placenta
14	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr14:78154400-78168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
20	chr14:78154600-78167200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:78155600-78164000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:78155600-78164800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:78155800-78165600	Strong transcription	Primary T cells from cord blood	blood
24	chr14:78156000-78171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:78156200-78164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:78156200-78165000	Strong transcription	Primary B cells from cord blood	blood
27	chr14:78156200-78165200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:78156200-78165800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr14:78156200-78172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr14:78156400-78164400	Strong transcription	Thymus	Thymus
31	chr14:78156600-78171800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr14:78156800-78164000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:78156800-78164200	Strong transcription	Fetal Intestine Large	intestine
34	chr14:78156800-78170000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:78156800-78171400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:78156800-78172400	Strong transcription	Dnd41	blood
37	chr14:78157400-78164800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr14:78157600-78164000	Strong transcription	Brain Anterior Caudate	brain
39	chr14:78157800-78164000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:78157800-78164000	Strong transcription	Fetal Lung	lung
41	chr14:78157800-78165000	Strong transcription	Brain Germinal Matrix	brain
42	chr14:78157800-78166200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:78158000-78164200	Strong transcription	HepG2	liver
44	chr14:78158400-78164000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr14:78158400-78164200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:78158600-78172800	Weak transcription	NHDF-Ad	bronchial
47	chr14:78159000-78164600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr14:78159000-78167800	Weak transcription	Gastric	stomach
49	chr14:78159600-78165200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr14:78159800-78164000	Strong transcription	Primary hematopoietic stem cells	blood

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