Variant report

Variant	rs9370233
Chromosome Location	chr6:53684912-53684913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53658699..53661103-chr6:53683402..53686266,2	MCF-7	breast:
2	chr6:53671854..53673444-chr6:53682878..53685695,2	MCF-7	breast:
3	chr6:53680007..53681550-chr6:53684589..53687118,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10456672	0.81[AMR][1000 genomes]
rs10755766	0.83[AMR][1000 genomes]
rs1076701	0.94[CEU][hapmap]
rs1076702	0.94[CEU][hapmap]
rs10948775	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11751003	0.80[AMR][1000 genomes]
rs11758147	0.81[AMR][1000 genomes]
rs13216331	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs2073020	0.85[AMR][1000 genomes]
rs2294789	0.81[EUR][1000 genomes]
rs2294790	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2294791	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3777661	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4278019	0.80[ASN][1000 genomes]
rs4314499	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4345397	0.82[AMR][1000 genomes]
rs4373352	0.83[AMR][1000 genomes]
rs4400206	0.81[AMR][1000 genomes]
rs4404762	0.83[AMR][1000 genomes]
rs4441952	0.81[AMR][1000 genomes]
rs4455653	0.85[ASN][1000 genomes]
rs4457161	0.80[AMR][1000 genomes]
rs4516937	0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs4563705	0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes]
rs4610551	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4712043	0.80[AMR][1000 genomes]
rs4715418	0.80[AMR][1000 genomes]
rs6903399	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6908232	0.82[AMR][1000 genomes]
rs6925356	0.80[AMR][1000 genomes]
rs6934324	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs7749273	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs7763482	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs7776124	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs9349685	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9357776	0.94[CEU][hapmap]
rs9357778	0.81[AMR][1000 genomes]
rs9370241	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370244	0.85[AMR][1000 genomes]
rs9370246	0.81[AMR][1000 genomes]
rs9382231	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9382232	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9382233	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9382235	0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9382238	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382241	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9382243	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382244	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382246	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382248	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9382252	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382253	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382254	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382256	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9395876	0.83[AMR][1000 genomes]
rs9395878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9395881	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9474641	0.80[AMR][1000 genomes]
rs9474646	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
7	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
9	chr6:53679400-53685200	Weak transcription	Gastric	stomach
10	chr6:53680400-53685800	Weak transcription	Brain Angular Gyrus	brain
11	chr6:53680400-53690000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:53680400-53690200	Weak transcription	Fetal Thymus	thymus
13	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
15	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:53680600-53687000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:53680600-53689400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:53680800-53687200	Weak transcription	Fetal Kidney	kidney
20	chr6:53680800-53689600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:53681000-53687200	Weak transcription	Aorta	Aorta
22	chr6:53681200-53685000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:53681200-53689800	Weak transcription	Osteobl	bone
24	chr6:53681400-53686800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:53682200-53687000	Weak transcription	Fetal Brain Female	brain
26	chr6:53682600-53689400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:53683000-53686200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:53683600-53685000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:53683600-53685000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:53683600-53685000	Enhancers	NHEK	skin
31	chr6:53683600-53689800	Weak transcription	Dnd41	blood
32	chr6:53683800-53687200	Enhancers	Brain Hippocampus Middle	brain
33	chr6:53684000-53685000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:53684000-53685800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:53684000-53687200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:53684000-53687400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:53684000-53687600	Weak transcription	Psoas Muscle	Psoas
38	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
39	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
40	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
42	chr6:53684200-53689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:53684400-53685200	Weak transcription	Brain Anterior Caudate	brain
44	chr6:53684400-53687000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:53684600-53686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:53684600-53690600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
48	chr6:53684800-53688200	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:53684800-53689800	Weak transcription	HMEC	breast

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