Variant report

Variant	rs6679661
Chromosome Location	chr1:223567267-223567268
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	chr1:223534957..223537393-chr1:223566287..223567830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10907375	0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11261265	0.96[EUR][1000 genomes]
rs11261268	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11261269	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12064476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074609	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12074782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12078619	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12087387	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12094897	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405882	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1400964	0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1621030	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1713213	0.89[CHB][hapmap]
rs17162005	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17163836	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1914612	1.00[ASW][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2298063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353204	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2501982	0.93[EUR][1000 genomes]
rs2678369	0.90[CHB][hapmap]
rs2678370	0.81[CHB][hapmap]
rs28788929	0.90[ASN][1000 genomes]
rs28897212	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34482638	0.84[AMR][1000 genomes]
rs35059272	0.84[AMR][1000 genomes]
rs35345617	1.00[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35727959	1.00[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35736338	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35996176	0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59584296	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838211	0.84[AMR][1000 genomes]
rs61838232	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61838233	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61838244	0.84[ASN][1000 genomes]
rs61838245	0.82[ASN][1000 genomes]
rs6661314	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6677044	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682552	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700523	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6701453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs825143	0.81[CHB][hapmap]
rs825148	0.90[CHB][hapmap]
rs866637	0.90[CHB][hapmap]

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	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv4687	chr1:223565080-223610362	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv517708	chr1:223567267-223567803	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223566600-223567400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:223566600-223567400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
3	chr1:223566600-223567400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:223566600-223567400	Bivalent/Poised TSS	Colonic Mucosa	Colon
5	chr1:223566600-223567400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
6	chr1:223566600-223567400	Bivalent/Poised TSS	A549	lung
7	chr1:223566600-223567400	Flanking Bivalent TSS/Enh	HMEC	breast
8	chr1:223566600-223567600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:223566800-223567400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:223566800-223567400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
11	chr1:223566800-223567400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:223566800-223567400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:223566800-223567400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:223566800-223567400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
15	chr1:223566800-223567400	Active TSS	HSMM	muscle
16	chr1:223566800-223567600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
17	chr1:223566800-223568600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:223567000-223567400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
19	chr1:223567000-223567400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:223567000-223567400	Enhancers	Fetal Heart	heart
21	chr1:223567000-223567400	Enhancers	Gastric	stomach
22	chr1:223567000-223567600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:223567200-223567400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:223567200-223567400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:223567200-223567400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:223567200-223567400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:223567200-223567400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:223567200-223567400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:223567200-223567400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:223567200-223567400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:223567200-223567400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:223567200-223567400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:223567200-223567400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:223567200-223567400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
35	chr1:223567200-223567400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr1:223567200-223567400	Flanking Active TSS	Esophagus	oesophagus
37	chr1:223567200-223567400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr1:223567200-223567400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr1:223567200-223567400	Enhancers	Pancreas	Pancrea
40	chr1:223567200-223567400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
41	chr1:223567200-223567400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
42	chr1:223567200-223567400	Bivalent Enhancer	NH-A	brain
43	chr1:223567200-223567600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr1:223567200-223567600	Bivalent Enhancer	Right Ventricle	heart
45	chr1:223567200-223567600	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr1:223567200-223568000	ZNF genes & repeats	Lung	lung

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