Variant report

Variant	rs9382238
Chromosome Location	chr6:53665698-53665699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53664733..53666465-chr6:53680416..53681978,2	MCF-7	breast:
2	chr6:53658074..53661500-chr6:53665501..53670163,6	MCF-7	breast:
3	chr6:53664494..53666032-chr6:53727700..53729812,2	MCF-7	breast:
4	chr6:53663341..53666059-chr6:53671400..53673766,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456672	0.84[AMR][1000 genomes]
rs10755766	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10948775	0.85[AMR][1000 genomes]
rs11751003	0.83[AMR][1000 genomes]
rs11758147	0.84[AMR][1000 genomes]
rs13216331	0.83[AMR][1000 genomes]
rs2073020	0.83[AMR][1000 genomes]
rs2294790	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2294791	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3777661	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4314499	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4345397	0.85[AMR][1000 genomes]
rs4373352	0.85[AMR][1000 genomes]
rs4400206	0.84[AMR][1000 genomes]
rs4404762	0.85[AMR][1000 genomes]
rs4441952	0.84[AMR][1000 genomes]
rs4457161	0.83[AMR][1000 genomes]
rs4516937	0.85[AMR][1000 genomes]
rs4563705	0.85[AMR][1000 genomes]
rs4610551	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4712043	0.83[AMR][1000 genomes]
rs4712044	0.82[AMR][1000 genomes]
rs4715418	0.83[AMR][1000 genomes]
rs6903399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6908232	0.85[AMR][1000 genomes]
rs6925356	0.83[AMR][1000 genomes]
rs6934324	0.84[AMR][1000 genomes]
rs7749273	0.82[AMR][1000 genomes]
rs7763482	0.84[AMR][1000 genomes]
rs7776124	0.82[AMR][1000 genomes]
rs9349685	0.87[EUR][1000 genomes]
rs9370233	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370241	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9370244	0.83[AMR][1000 genomes]
rs9382231	0.83[AMR][1000 genomes]
rs9382232	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382233	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382235	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382241	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382243	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382244	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382246	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382248	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9382252	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382253	0.85[EUR][1000 genomes]
rs9382254	0.85[EUR][1000 genomes]
rs9382256	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395876	0.85[AMR][1000 genomes]
rs9395878	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395881	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9474641	0.83[AMR][1000 genomes]
rs9474646	0.85[AMR][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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
3	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53661400-53668000	Weak transcription	Ovary	ovary
6	chr6:53661400-53669800	Weak transcription	Gastric	stomach
7	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
10	chr6:53661600-53665800	Weak transcription	NHLF	lung
11	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:53662200-53665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:53662400-53668000	Weak transcription	NH-A	brain
16	chr6:53662600-53665800	Weak transcription	Brain Anterior Caudate	brain
17	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
20	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
22	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
23	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
24	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:53662800-53668000	Weak transcription	NHEK	skin
27	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:53662800-53669800	Weak transcription	HMEC	breast
29	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
30	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
34	chr6:53664000-53668000	Weak transcription	HUVEC	blood vessel
35	chr6:53664000-53669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:53664600-53666000	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:53664800-53665800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:53664800-53665800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:53664800-53667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:53664800-53668400	Weak transcription	HepG2	liver
41	chr6:53664800-53669800	Weak transcription	Fetal Thymus	thymus
42	chr6:53664800-53673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:53665000-53665800	Weak transcription	Dnd41	blood
44	chr6:53665000-53667800	Weak transcription	Brain Substantia Nigra	brain
45	chr6:53665000-53669800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:53665000-53674800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:53665400-53666000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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