Variant report

Variant	rs6663726
Chromosome Location	chr1:228344000-228344001
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	chr1:228282033..228284613-chr1:228342310..228344410,2	MCF-7	breast:
2	chr1:228343198..228344704-chr1:228404539..228407474,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10127705	0.90[EUR][1000 genomes]
rs1034792	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs10495278	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10495279	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10916266	0.90[EUR][1000 genomes]
rs1094602	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1094603	0.90[EUR][1000 genomes]
rs11577976	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11580599	0.86[EUR][1000 genomes]
rs11581037	1.00[CEU][hapmap]
rs11581169	0.90[EUR][1000 genomes]
rs11584418	1.00[CEU][hapmap]
rs11586055	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1188975	0.85[CHB][hapmap]
rs1188977	0.88[ASW][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap]
rs12034268	0.86[EUR][1000 genomes]
rs12039801	0.86[EUR][1000 genomes]
rs12088423	1.00[CEU][hapmap]
rs12740965	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1620734	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs1803695	0.90[EUR][1000 genomes]
rs28587961	0.90[EUR][1000 genomes]
rs34687764	0.90[EUR][1000 genomes]
rs3795773	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795774	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs41303083	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653533	0.85[CHB][hapmap]
rs4653906	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653908	0.86[EUR][1000 genomes]
rs4653909	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653914	0.86[EUR][1000 genomes]
rs61825156	0.90[EUR][1000 genomes]
rs61825157	0.86[EUR][1000 genomes]
rs61825159	0.86[EUR][1000 genomes]
rs61827462	0.86[EUR][1000 genomes]
rs6668719	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];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708126	0.85[CHB][hapmap]
rs7530253	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537552	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539664	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap]
rs822727	0.85[CHB][hapmap]
rs9287011	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs9970544	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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 miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
17	nsv549291	chr1:228338939-228350774	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv873261	chr1:228338939-228359775	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
19	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
20	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
21	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
22	esv3358217	chr1:228341829-228346127	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228332800-228349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:228333200-228344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:228333800-228350400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:228336800-228350200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:228337200-228344400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:228337800-228349800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:228338000-228344000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:228338000-228349200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228338000-228349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:228338200-228344800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:228338200-228344800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:228338200-228352400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:228338400-228349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:228339000-228344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:228339000-228346000	Weak transcription	HMEC	breast
16	chr1:228339400-228344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:228339400-228344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:228339400-228345000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:228339400-228352600	Weak transcription	Brain Anterior Caudate	brain
20	chr1:228339600-228344000	Weak transcription	Adipose Nuclei	Adipose
21	chr1:228339600-228345600	Weak transcription	Right Atrium	heart
22	chr1:228339600-228349000	Weak transcription	NHLF	lung
23	chr1:228339800-228349400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:228340000-228344000	Weak transcription	Liver	Liver
25	chr1:228340000-228349200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:228340200-228345200	Weak transcription	Right Ventricle	heart
27	chr1:228340600-228349600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:228341000-228344200	Enhancers	Fetal Thymus	thymus
29	chr1:228341600-228344400	Enhancers	Thymus	Thymus
30	chr1:228341800-228344000	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:228341800-228345400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:228342000-228344200	Enhancers	Primary T cells from cord blood	blood
33	chr1:228342000-228344200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:228342000-228344400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:228342200-228345200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:228342600-228344200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:228342600-228344200	Enhancers	Esophagus	oesophagus
38	chr1:228342600-228344200	Enhancers	Hela-S3	cervix
39	chr1:228342600-228350000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:228342800-228344000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:228342800-228344000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:228342800-228344000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr1:228342800-228344400	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr1:228342800-228345800	Enhancers	Lung	lung
45	chr1:228342800-228346400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:228343000-228344000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:228343000-228344200	Enhancers	Fetal Heart	heart
48	chr1:228343000-228347200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:228343200-228345600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:228343200-228349200	Weak transcription	K562	blood

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