Variant report

Variant	rs2885195
Chromosome Location	chr3:143568223-143568224
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	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10513218	1.00[CHB][hapmap]
rs11714060	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1319100	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1319101	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1394398	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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394402	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1504603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1504604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1979911	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1995529	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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011290	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2011297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2011303	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2361202	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2361203	0.83[EUR][1000 genomes]
rs2361205	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2361207	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2361209	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4286430	1.00[CEU][hapmap]
rs4499594	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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4839672	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4839673	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs56220620	1.00[ASN][1000 genomes]
rs56407400	1.00[ASN][1000 genomes]
rs57718888	1.00[ASN][1000 genomes]
rs58887384	1.00[ASN][1000 genomes]
rs58921154	1.00[ASN][1000 genomes]
rs59306133	1.00[ASN][1000 genomes]
rs60249173	0.85[ASN][1000 genomes]
rs60523819	1.00[ASN][1000 genomes]
rs60550983	0.85[ASN][1000 genomes]
rs6440195	1.00[CEU][hapmap]
rs6440196	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6768399	1.00[CHB][hapmap]
rs6768702	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6782974	1.00[CEU][hapmap]
rs6794907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73869037	0.85[ASN][1000 genomes]
rs73869039	0.85[ASN][1000 genomes]
rs73869041	0.85[ASN][1000 genomes]
rs73869042	1.00[ASN][1000 genomes]
rs73869048	1.00[ASN][1000 genomes]
rs73869049	1.00[ASN][1000 genomes]
rs73869050	1.00[ASN][1000 genomes]
rs73871822	1.00[ASN][1000 genomes]
rs73871823	1.00[ASN][1000 genomes]
rs73871826	1.00[ASN][1000 genomes]
rs73871827	1.00[ASN][1000 genomes]
rs7434217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7613146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7623477	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7627020	0.89[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7637640	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7645681	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7653164	1.00[CHB][hapmap]
rs9289669	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9824974	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870661	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2885195	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:143566000-143568400	Active TSS	Ovary	ovary
3	chr3:143566200-143568600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:143567400-143568400	Enhancers	Fetal Thymus	thymus
5	chr3:143567400-143568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:143567400-143569000	Enhancers	HSMM	muscle
7	chr3:143567400-143569000	Enhancers	NHEK	skin
8	chr3:143567400-143570000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:143567400-143570600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:143567400-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:143567600-143568400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr3:143567600-143568400	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr3:143567600-143569000	Enhancers	HMEC	breast
14	chr3:143567600-143569200	Enhancers	Fetal Stomach	stomach
15	chr3:143567600-143569200	Enhancers	HUVEC	blood vessel
16	chr3:143567600-143569400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:143567600-143569600	Enhancers	Primary T cells from cord blood	blood
18	chr3:143567600-143569600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:143567600-143569600	Enhancers	HSMMtube	muscle
20	chr3:143567800-143568400	Enhancers	Adipose Nuclei	Adipose
21	chr3:143567800-143568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:143567800-143568600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:143567800-143568600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:143567800-143568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:143567800-143568600	Weak transcription	Fetal Lung	lung
26	chr3:143567800-143568600	Weak transcription	Osteobl	bone
27	chr3:143567800-143568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:143567800-143568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:143567800-143568800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:143567800-143568800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:143567800-143569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:143567800-143569000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr3:143567800-143569000	Enhancers	NHLF	lung
34	chr3:143567800-143569200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:143567800-143569200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:143567800-143569200	Enhancers	NH-A	brain
37	chr3:143567800-143569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:143567800-143569600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:143567800-143569600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:143567800-143569600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:143567800-143569600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:143567800-143569600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr3:143567800-143569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:143567800-143569800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:143567800-143570000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:143567800-143570000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:143567800-143570200	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:143567800-143570400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:143567800-143571000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:143568000-143568400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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