Variant report

Variant	rs2284230
Chromosome Location	chr14:78015897-78015898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77922995..77924910-chr14:78015324..78017998,2	MCF-7	breast:
2	chr14:78013590..78016333-chr14:78173040..78175809,2	MCF-7	breast:
3	chr14:77841219..77843906-chr14:78015874..78017760,2	MCF-7	breast:
4	chr14:78013266..78015094-chr14:78015615..78018423,2	MCF-7	breast:
5	chr14:78014573..78016241-chr14:78173226..78176092,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240233	Chromatin interaction
ENSG00000100583	Chromatin interaction
ENSG00000119705	Chromatin interaction
ENSG00000100601	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000100580	Chromatin interaction
ENSG00000151445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10135955	0.83[CHB][hapmap]
rs10147810	0.84[JPT][hapmap]
rs12101129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586959	0.96[ASN][1000 genomes]
rs12589478	0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17105949	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2299911	0.83[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2299912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299915	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482839	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28654332	0.97[ASN][1000 genomes]
rs28676801	0.94[ASN][1000 genomes]
rs28716286	0.94[ASN][1000 genomes]
rs34359219	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55949800	0.97[ASN][1000 genomes]
rs56208416	0.89[ASN][1000 genomes]
rs61990763	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61992441	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72683251	0.82[ASN][1000 genomes]

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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2284230	C14orf148	cis	parietal	SCAN
rs2284230	RPS6KL1	cis	cerebellum	SCAN
rs2284230	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL
rs2284230	MLH3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77970200-78047200	Weak transcription	Fetal Heart	heart
2	chr14:77972000-78018000	Weak transcription	Hela-S3	cervix
3	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
4	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr14:77997800-78018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:78006800-78019000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:78008200-78019000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:78009600-78019400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr14:78009600-78021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
15	chr14:78010000-78016400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr14:78010000-78018800	Strong transcription	NH-A	brain
17	chr14:78010000-78019800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr14:78010000-78029800	Strong transcription	Primary T cells from cord blood	blood
19	chr14:78010200-78019000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr14:78010200-78020400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr14:78010200-78026800	Weak transcription	Stomach Mucosa	stomach
22	chr14:78010400-78017200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr14:78010400-78018600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr14:78010400-78030000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr14:78010600-78016400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:78010600-78017000	Strong transcription	Adipose Nuclei	Adipose
27	chr14:78010600-78017200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr14:78010600-78019200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr14:78010600-78025000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr14:78010800-78016400	Strong transcription	Primary B cells from cord blood	blood
31	chr14:78010800-78018600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr14:78010800-78019000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr14:78011000-78020000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr14:78011000-78031800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr14:78011200-78019000	Strong transcription	Osteobl	bone
36	chr14:78011200-78045800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:78011400-78019000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:78011400-78037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:78012000-78016400	Strong transcription	Liver	Liver
40	chr14:78012800-78019000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr14:78013000-78017400	Strong transcription	Small Intestine	intestine
42	chr14:78013000-78018800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr14:78013200-78030600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr14:78013400-78016200	Strong transcription	Left Ventricle	heart
46	chr14:78013400-78016400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:78013400-78016400	Strong transcription	Fetal Lung	lung
48	chr14:78013400-78016400	Strong transcription	NHDF-Ad	bronchial
49	chr14:78013400-78016800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr14:78013400-78017200	Strong transcription	Fetal Thymus	thymus

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