Variant report

Variant	rs72932336
Chromosome Location	chr2:86729091-86729092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86669073..86671790-chr2:86726789..86729265,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP3-1	chr2:86727619-86729774	ENSG00000248011

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1030886	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1030887	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11548929	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11899532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	0.89[EUR][1000 genomes]
rs1518812	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027280	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34605051	0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56227180	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56242451	0.89[EUR][1000 genomes]
rs56347930	0.91[EUR][1000 genomes]
rs56378606	0.90[EUR][1000 genomes]
rs57291816	0.91[EUR][1000 genomes]
rs57836876	0.89[EUR][1000 genomes]
rs58091125	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60810860	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.96[EUR][1000 genomes]
rs61547860	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710780	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930315	0.91[EUR][1000 genomes]
rs72930323	0.91[EUR][1000 genomes]
rs72930336	0.91[EUR][1000 genomes]
rs72930340	0.91[EUR][1000 genomes]
rs72930349	0.91[EUR][1000 genomes]
rs72930361	0.91[EUR][1000 genomes]
rs72930362	0.91[EUR][1000 genomes]
rs72930364	0.91[EUR][1000 genomes]
rs72930369	0.91[EUR][1000 genomes]
rs72930387	0.89[EUR][1000 genomes]
rs72930396	0.87[EUR][1000 genomes]
rs72930400	0.87[EUR][1000 genomes]
rs72932307	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932310	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932369	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585722	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7586028	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604179	1.00[EUR][1000 genomes]
rs7608800	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:86724000-86729600	ZNF genes & repeats	GM12878-XiMat	blood
6	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr2:86725200-86730000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:86725400-86730000	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:86725800-86729200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr2:86726000-86729200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:86726000-86729600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr2:86726000-86729600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:86726000-86729800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr2:86726000-86731200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:86726200-86729800	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr2:86726200-86729800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr2:86726400-86735400	Weak transcription	NHLF	lung
19	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
20	chr2:86726400-86741800	Weak transcription	NH-A	brain
21	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:86726600-86729400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
24	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
25	chr2:86726800-86739000	Weak transcription	K562	blood
26	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:86727200-86729400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr2:86727400-86731000	Weak transcription	Osteobl	bone
29	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
30	chr2:86727600-86731800	Weak transcription	HSMMtube	muscle
31	chr2:86727600-86732600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:86727600-86734600	Weak transcription	HMEC	breast
33	chr2:86727800-86732000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:86728000-86729200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:86728000-86729400	Strong transcription	Brain Substantia Nigra	brain
36	chr2:86728000-86729600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:86728000-86729600	Weak transcription	Fetal Thymus	thymus
38	chr2:86728000-86729600	Weak transcription	Small Intestine	intestine
39	chr2:86728000-86729800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:86728000-86730400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:86728000-86730600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:86728000-86730600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:86728000-86731000	Weak transcription	Esophagus	oesophagus
44	chr2:86728000-86731000	Weak transcription	Pancreas	Pancrea
45	chr2:86728000-86731800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:86728000-86731800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:86728000-86732000	Weak transcription	Brain Angular Gyrus	brain
48	chr2:86728000-86732000	Weak transcription	Fetal Kidney	kidney
49	chr2:86728000-86732000	Weak transcription	Gastric	stomach
50	chr2:86728000-86732400	Weak transcription	H1 Cell Line	embryonic stem cell

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