Variant report

Variant	rs2972940
Chromosome Location	chr5:37743329-37743330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10055929	0.83[AMR][1000 genomes]
rs10058348	1.00[AMR][1000 genomes]
rs10064268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10067274	1.00[AMR][1000 genomes]
rs10069946	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10071998	0.83[AMR][1000 genomes]
rs10072096	1.00[AMR][1000 genomes]
rs10072199	1.00[AMR][1000 genomes]
rs10074395	1.00[AMR][1000 genomes]
rs10075048	1.00[AMR][1000 genomes]
rs11954051	0.83[AMR][1000 genomes]
rs11957206	0.83[AMR][1000 genomes]
rs11957694	1.00[AMR][1000 genomes]
rs13358095	1.00[AMR][1000 genomes]
rs13359573	0.83[AMR][1000 genomes]
rs13436949	1.00[AMR][1000 genomes]
rs2973065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2973071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2973072	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2973073	0.83[AMR][1000 genomes]
rs34034635	0.83[AMR][1000 genomes]
rs7709443	0.83[AMR][1000 genomes]
rs7723792	0.83[AMR][1000 genomes]
rs7730584	1.00[AMR][1000 genomes]
rs7737381	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9292667	0.83[AMR][1000 genomes]
rs983657	1.00[AMR][1000 genomes]
rs983658	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37697000-37743800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:37717800-37756200	Weak transcription	Right Ventricle	heart
3	chr5:37718400-37745400	Weak transcription	Pancreas	Pancrea
4	chr5:37718400-37755800	Weak transcription	Spleen	Spleen
5	chr5:37721400-37764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:37727600-37745400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:37728000-37757200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:37728000-37758800	Weak transcription	Brain Germinal Matrix	brain
9	chr5:37728400-37745400	Weak transcription	Thymus	Thymus
10	chr5:37728800-37754400	Weak transcription	Placenta	Placenta
11	chr5:37729000-37746000	Weak transcription	Fetal Thymus	thymus
12	chr5:37729400-37753200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:37729600-37745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:37729600-37755800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:37730000-37749800	Weak transcription	HepG2	liver
16	chr5:37730200-37752000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:37730200-37757000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:37730400-37752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:37731400-37745400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:37731600-37745600	Weak transcription	Fetal Lung	lung
21	chr5:37735800-37744600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr5:37736200-37752200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:37736200-37752400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr5:37736400-37744000	Weak transcription	Fetal Brain Male	brain
25	chr5:37737400-37744600	Strong transcription	Primary T cells from cord blood	blood
26	chr5:37737800-37754000	Weak transcription	Left Ventricle	heart
27	chr5:37738400-37744400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:37738400-37757200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:37738600-37745200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:37738800-37756400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:37738800-37757400	Weak transcription	Brain Anterior Caudate	brain
32	chr5:37739000-37743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:37739000-37757200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:37739200-37751200	Weak transcription	NHEK	skin
35	chr5:37739200-37757600	Weak transcription	A549	lung
36	chr5:37739400-37751200	Weak transcription	HMEC	breast
37	chr5:37739400-37752800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:37739600-37747400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr5:37739600-37748400	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:37739600-37757200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:37740200-37743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:37740800-37743800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:37740800-37743800	Weak transcription	Hela-S3	cervix
44	chr5:37740800-37756200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:37741000-37746200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:37741200-37744800	Weak transcription	NHLF	lung
47	chr5:37741200-37757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:37741600-37743800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:37741800-37745200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr5:37741800-37751200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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