Variant report

Variant	rs1255960
Chromosome Location	chr14:64542872-64542873
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	chr14:64539092..64541839-chr14:64542206..64544717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10135588	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10140978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10146667	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10151127	0.87[CHD][hapmap]
rs11622858	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11844088	0.82[ASN][1000 genomes]
rs11844628	0.82[ASN][1000 genomes]
rs1255948	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255950	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255951	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255952	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255955	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1255959	0.82[CHB][hapmap]
rs1255961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs1255968	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586503	0.82[ASN][1000 genomes]
rs1262241	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12894671	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17101419	0.82[CEU][hapmap]
rs1890907	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1890908	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153477	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2153478	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2153481	0.87[ASN][1000 genomes]
rs2781377	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2781378	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866737	0.82[ASN][1000 genomes]
rs4027405	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4899131	0.82[ASN][1000 genomes]
rs6573542	0.82[ASN][1000 genomes]
rs6573544	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7146859	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147157	0.82[ASN][1000 genomes]
rs7150982	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153376	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7157993	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8007972	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:64481400-64574000	Weak transcription	Stomach Mucosa	stomach
3	chr14:64489400-64568600	Weak transcription	Small Intestine	intestine
4	chr14:64491200-64565200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:64492200-64547400	Weak transcription	Colonic Mucosa	Colon
6	chr14:64519400-64592000	Weak transcription	Fetal Brain Male	brain
7	chr14:64519600-64545200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr14:64525400-64566600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr14:64526000-64552200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr14:64526800-64577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:64527000-64547200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:64527600-64551800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:64527800-64549000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:64527800-64552000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:64527800-64556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:64528000-64557000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr14:64528000-64567400	Weak transcription	Fetal Heart	heart
18	chr14:64528400-64547000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:64529000-64553200	Strong transcription	Dnd41	blood
20	chr14:64529400-64543000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr14:64529400-64566800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:64536200-64543000	Strong transcription	Brain Germinal Matrix	brain
23	chr14:64536800-64546400	Weak transcription	Fetal Brain Female	brain
24	chr14:64536800-64552200	Strong transcription	Placenta	Placenta
25	chr14:64537400-64543000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:64537400-64543000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr14:64537400-64543000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr14:64538600-64543200	Strong transcription	Fetal Lung	lung
29	chr14:64538600-64543400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:64539600-64549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:64539600-64552400	Weak transcription	Brain Anterior Caudate	brain
32	chr14:64540400-64544000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:64540800-64545600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr14:64541200-64543000	Enhancers	NHDF-Ad	bronchial
35	chr14:64541200-64545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:64541200-64547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:64541200-64547400	Weak transcription	Right Ventricle	heart
38	chr14:64541400-64545000	Weak transcription	Primary B cells from cord blood	blood
39	chr14:64541400-64547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:64541400-64549200	Weak transcription	Psoas Muscle	Psoas
41	chr14:64541600-64545200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr14:64541600-64545400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:64541600-64545400	Weak transcription	Fetal Stomach	stomach
44	chr14:64541600-64546400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr14:64541600-64546400	Weak transcription	Ovary	ovary
46	chr14:64541600-64546800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr14:64541600-64547000	Weak transcription	Spleen	Spleen
48	chr14:64541600-64547200	Weak transcription	Esophagus	oesophagus
49	chr14:64541600-64547400	Weak transcription	Aorta	Aorta
50	chr14:64541600-64547400	Weak transcription	Gastric	stomach

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