Variant report

Variant	rs3000999
Chromosome Location	chr6:53670645-53670646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53668227..53671026-chr6:53671811..53674151,2	MCF-7	breast:
2	chr6:53669263..53671782-chr6:53791090..53793404,2	MCF-7	breast:
3	chr6:53657464..53661441-chr6:53668474..53671433,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.88[EUR][1000 genomes]
rs13220665	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001010	0.92[EUR][1000 genomes]
rs3003489	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003491	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3003500	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3003501	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34165049	0.82[EUR][1000 genomes]
rs34861916	0.88[EUR][1000 genomes]
rs34880762	0.88[EUR][1000 genomes]
rs35389351	0.89[EUR][1000 genomes]
rs35517171	0.88[EUR][1000 genomes]
rs35756855	0.85[EUR][1000 genomes]
rs3813849	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236115	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4276502	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4336450	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4382260	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4398733	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4437471	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4489155	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4591854	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4615391	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4712048	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4712049	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4715424	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs4715426	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59641455	0.88[EUR][1000 genomes]
rs60035355	0.88[EUR][1000 genomes]
rs6458957	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458959	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458961	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6458962	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6458965	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458969	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650996	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6899752	0.88[EUR][1000 genomes]
rs6901644	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.88[EUR][1000 genomes]
rs6926478	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937901	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.88[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs7762883	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7763081	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7769893	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9382237	0.98[EUR][1000 genomes]
rs9382250	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3430400	chr6:53668793-53672091	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
3	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
4	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:53664800-53673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:53665000-53674800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:53667800-53673600	Enhancers	Brain Substantia Nigra	brain
10	chr6:53668000-53670800	Enhancers	NHEK	skin
11	chr6:53668000-53671400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
13	chr6:53668600-53674400	Enhancers	Brain Hippocampus Middle	brain
14	chr6:53668800-53674400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:53668800-53674800	Weak transcription	Lung	lung
16	chr6:53668800-53676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:53668800-53676000	Weak transcription	HUVEC	blood vessel
18	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:53668800-53683800	Weak transcription	Ovary	ovary
20	chr6:53669000-53670800	Weak transcription	HepG2	liver
21	chr6:53669400-53671000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:53669400-53671400	Enhancers	Brain Anterior Caudate	brain
23	chr6:53669600-53671000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:53669600-53671400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:53669600-53672200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:53669600-53674000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:53669800-53670800	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:53669800-53670800	Enhancers	Right Atrium	heart
29	chr6:53669800-53670800	Enhancers	Stomach Smooth Muscle	stomach
30	chr6:53669800-53670800	Enhancers	Dnd41	blood
31	chr6:53669800-53670800	Enhancers	HMEC	breast
32	chr6:53669800-53671000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr6:53669800-53671000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:53669800-53671200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:53669800-53671400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:53669800-53671400	Enhancers	Fetal Thymus	thymus
37	chr6:53669800-53671400	Enhancers	Pancreas	Pancrea
38	chr6:53669800-53671600	Enhancers	Gastric	stomach
39	chr6:53669800-53676800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:53670000-53670800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:53670000-53671000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr6:53670000-53671000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:53670000-53671000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:53670000-53671000	Enhancers	Esophagus	oesophagus
45	chr6:53670000-53671400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:53670000-53671400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:53670000-53671400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:53670000-53671400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr6:53670000-53671400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:53670000-53671800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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