Variant report

Variant	rs256975
Chromosome Location	chr5:114893223-114893224
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	chr5:114879154..114881611-chr5:114889489..114893270,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10077825	1.00[CEU][hapmap]
rs11740401	0.82[ASN][1000 genomes]
rs1363550	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1422641	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1422642	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1422643	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1422644	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1592942	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1592943	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17137937	0.90[ASN][1000 genomes]
rs17138030	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs185379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895283	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194398	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2052504	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2052505	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288384	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2431600	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2546473	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546483	1.00[CEU][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256946	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256958	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256960	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256961	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256966	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256973	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256979	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256981	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256982	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256983	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256985	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256992	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2597	0.92[ASN][1000 genomes]
rs2617441	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4920867	0.92[ASN][1000 genomes]
rs4920869	0.86[ASN][1000 genomes]
rs57010629	0.84[ASN][1000 genomes]
rs60640600	0.88[ASN][1000 genomes]
rs73254600	0.84[ASN][1000 genomes]
rs73782714	0.84[ASN][1000 genomes]
rs9326965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9968571	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs256975	TICAM2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114887600-114893800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114887800-114893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:114889000-114893600	Weak transcription	NHDF-Ad	bronchial
4	chr5:114889400-114895600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:114891000-114893600	Weak transcription	NHLF	lung
6	chr5:114891200-114893600	Weak transcription	HepG2	liver
7	chr5:114891200-114895600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:114891800-114893400	Enhancers	Lung	lung
9	chr5:114892200-114893600	Enhancers	Gastric	stomach
10	chr5:114892200-114894000	Enhancers	Pancreas	Pancrea
11	chr5:114892400-114895800	Enhancers	HUVEC	blood vessel
12	chr5:114892600-114893600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:114892600-114894000	Enhancers	Fetal Thymus	thymus
14	chr5:114892600-114894200	Enhancers	Primary T cells from cord blood	blood
15	chr5:114892600-114894200	Enhancers	Dnd41	blood
16	chr5:114892600-114897200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:114892800-114893400	Enhancers	Primary hematopoietic stem cells	blood
18	chr5:114892800-114894000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:114892800-114894000	Enhancers	Right Atrium	heart
20	chr5:114892800-114894200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:114892800-114896200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr5:114893000-114894000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr5:114893000-114894000	Enhancers	Placenta	Placenta
24	chr5:114893000-114894000	Enhancers	Thymus	Thymus
25	chr5:114893000-114894200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr5:114893000-114894200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:114893000-114894200	Enhancers	Brain Anterior Caudate	brain
28	chr5:114893000-114894600	Enhancers	Stomach Mucosa	stomach
29	chr5:114893000-114894800	Enhancers	Liver	Liver
30	chr5:114893200-114893600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:114893200-114893600	Enhancers	Colonic Mucosa	Colon
32	chr5:114893200-114894000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr5:114893200-114894000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:114893200-114894000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:114893200-114894000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:114893200-114894000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:114893200-114894000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:114893200-114894000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr5:114893200-114894000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:114893200-114894000	Enhancers	Duodenum Mucosa	Duodenum
41	chr5:114893200-114894000	Enhancers	Esophagus	oesophagus
42	chr5:114893200-114894000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr5:114893200-114894000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:114893200-114894200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:114893200-114894200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:114893200-114894200	Enhancers	Right Ventricle	heart
47	chr5:114893200-114894400	Enhancers	HSMMtube	muscle
48	chr5:114893200-114894600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:114893200-114896000	Enhancers	Osteobl	bone

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