Variant report

Variant	rs4276504
Chromosome Location	chr6:53675115-53675116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53658844..53661174-chr6:53672995..53675908,3	MCF-7	breast:
2	chr6:53657579..53660733-chr6:53674241..53678049,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10498795	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1543356	1.00[CHB][hapmap]
rs16884427	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17748452	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223617	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2473603	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2820217	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2820218	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs4077760	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4131378	0.86[EUR][1000 genomes]
rs4272222	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4357137	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4380749	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4397225	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4476827	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4580851	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6905927	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6908101	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6919924	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6925165	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs761135	1.00[CHB][hapmap]
rs7752696	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9474672	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	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

No data

Chromatin state (count:73 , 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	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
8	chr6:53668800-53676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:53668800-53676000	Weak transcription	HUVEC	blood vessel
10	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:53668800-53683800	Weak transcription	Ovary	ovary
12	chr6:53669800-53676800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:53670200-53675600	Weak transcription	Left Ventricle	heart
14	chr6:53670200-53678000	Weak transcription	Aorta	Aorta
15	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:53670400-53675600	Weak transcription	Fetal Intestine Large	intestine
17	chr6:53670400-53676000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:53670800-53676000	Weak transcription	Right Atrium	heart
19	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:53671000-53675600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:53671000-53675600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:53671000-53675600	Weak transcription	Esophagus	oesophagus
24	chr6:53671000-53676400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:53671200-53675600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:53671200-53675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
30	chr6:53671400-53675600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:53671400-53675600	Weak transcription	Primary T cells from cord blood	blood
32	chr6:53671400-53675600	Weak transcription	Pancreas	Pancrea
33	chr6:53671400-53675800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:53671400-53676000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:53671400-53676000	Weak transcription	Brain Anterior Caudate	brain
36	chr6:53671400-53676400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:53671600-53676200	Weak transcription	Gastric	stomach
39	chr6:53671800-53675800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:53672200-53676000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:53672600-53675600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:53673000-53678400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:53673600-53675600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:53673600-53676000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:53673600-53676000	Weak transcription	Fetal Heart	heart
47	chr6:53673600-53677800	Weak transcription	Brain Substantia Nigra	brain
48	chr6:53673600-53682800	Weak transcription	Dnd41	blood
49	chr6:53673800-53675600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:53673800-53675600	Weak transcription	Brain Angular Gyrus	brain

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