Variant report

Variant	rs3003496
Chromosome Location	chr6:53677308-53677309
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53657579..53660733-chr6:53674241..53678049,6	MCF-7	breast:
2	chr6:53588027..53590620-chr6:53675669..53678421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13197492	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3000998	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3001003	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3003497	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4269375	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4276503	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4342426	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4475321	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4587161	0.80[EUR][1000 genomes]
rs4715425	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5001609	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6458960	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6458970	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6900929	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9367542	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9370236	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9382239	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
3	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
5	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:53668800-53683800	Weak transcription	Ovary	ovary
7	chr6:53670200-53678000	Weak transcription	Aorta	Aorta
8	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
14	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:53673000-53678400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:53673600-53677800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:53673600-53682800	Weak transcription	Dnd41	blood
19	chr6:53673800-53678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:53674200-53678200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53674800-53678400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:53674800-53679600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
24	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
25	chr6:53675400-53679000	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
27	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:53675600-53678200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:53675600-53678800	Enhancers	Hela-S3	cervix
30	chr6:53676200-53677800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:53676200-53677800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:53676200-53677800	Weak transcription	Lung	lung
33	chr6:53676200-53678000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:53676200-53678400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:53676200-53678600	Enhancers	Esophagus	oesophagus
36	chr6:53676200-53678800	Enhancers	Gastric	stomach
37	chr6:53676200-53679200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:53676200-53683600	Weak transcription	Left Ventricle	heart
39	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:53676400-53677600	Weak transcription	Brain Anterior Caudate	brain
41	chr6:53676400-53677600	Weak transcription	Brain Germinal Matrix	brain
42	chr6:53676400-53677600	Weak transcription	Colonic Mucosa	Colon
43	chr6:53676400-53677800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:53676400-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:53676400-53678400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:53676400-53679200	Weak transcription	Brain Angular Gyrus	brain
47	chr6:53676400-53679800	Weak transcription	Fetal Heart	heart
48	chr6:53676600-53677600	Weak transcription	HepG2	liver
49	chr6:53676600-53677800	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:53676600-53677800	Weak transcription	HUVEC	blood vessel

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