Variant report

Variant	rs2336660
Chromosome Location	chr3:52896731-52896732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11130329	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2336661	1.00[YRI][hapmap]
rs2336662	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535624	0.85[AMR][1000 genomes]
rs2710336	0.81[YRI][hapmap]
rs4687561	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773441	1.00[YRI][hapmap]
rs6787916	0.85[AMR][1000 genomes]
rs6798472	1.00[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:52886200-52907800	Weak transcription	NHLF	lung
6	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
8	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52886600-52899800	Weak transcription	Dnd41	blood
11	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
15	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
17	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
22	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:52887600-52898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
25	chr3:52888000-52898000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:52889000-52897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:52889200-52898200	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52890000-52896800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:52891400-52901600	Weak transcription	Right Atrium	heart
37	chr3:52891600-52909400	Weak transcription	Ovary	ovary
38	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
39	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
42	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
44	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:52894800-52897000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:52894800-52899800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:52895000-52898600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:52895200-52900400	Weak transcription	Lung	lung

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