Variant report

Variant	rs2972241
Chromosome Location	chr5:80894982-80894983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2917541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2917543	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917545	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2921499	0.81[CHB][hapmap]
rs2972227	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972237	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972239	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972245	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2973335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973336	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973341	0.81[AFR][1000 genomes]
rs2973345	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973347	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2973350	1.00[YRI][hapmap]
rs383082	0.87[AMR][1000 genomes]
rs388560	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3943733	0.80[CHB][hapmap]
rs401912	0.90[CHB][hapmap]
rs402390	0.90[CHB][hapmap]
rs406465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417684	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs433118	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4426897	1.00[YRI][hapmap]
rs447747	0.86[AMR][1000 genomes]
rs4519906	0.93[ASN][1000 genomes]
rs454578	0.85[CHB][hapmap]
rs62366265	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6452419	1.00[YRI][hapmap]
rs827074	0.87[AMR][1000 genomes];0.89[EUR][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	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972241	CTD-2249K22.1	cis	Thyroid	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:80883800-80909200	Weak transcription	HSMM	muscle
3	chr5:80885200-80905400	Weak transcription	Pancreas	Pancrea
4	chr5:80886800-80905400	Weak transcription	Brain Substantia Nigra	brain
5	chr5:80887000-80905600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:80887000-80922400	Weak transcription	Psoas Muscle	Psoas
7	chr5:80887200-80898000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:80887200-80905400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:80887200-80911200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:80887400-80904600	Weak transcription	Osteobl	bone
11	chr5:80888600-80905200	Weak transcription	Brain Germinal Matrix	brain
12	chr5:80888600-80905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:80888800-80897600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:80888800-80905600	Weak transcription	Fetal Stomach	stomach
15	chr5:80892000-80905600	Weak transcription	Gastric	stomach
16	chr5:80892800-80904600	Weak transcription	Fetal Brain Male	brain
17	chr5:80893000-80900400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:80893400-80898800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:80893400-80926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:80893600-80905600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:80893600-80905600	Weak transcription	Aorta	Aorta
22	chr5:80893600-80909600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:80893800-80895400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:80893800-80903000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:80894000-80895000	Strong transcription	Brain Hippocampus Middle	brain
26	chr5:80894000-80895200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:80894000-80895600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:80894000-80895800	ZNF genes & repeats	Dnd41	blood
29	chr5:80894000-80897800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:80894000-80901600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:80894200-80895000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:80894200-80895200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:80894200-80895400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr5:80894200-80895600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:80894200-80895600	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr5:80894200-80895600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr5:80894200-80895800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:80894200-80895800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr5:80894200-80899200	Strong transcription	Fetal Thymus	thymus
40	chr5:80894400-80895000	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr5:80894400-80895400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr5:80894400-80895600	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr5:80894400-80895800	Strong transcription	Fetal Lung	lung
44	chr5:80894400-80895800	Strong transcription	Thymus	Thymus
45	chr5:80894400-80905200	Weak transcription	Fetal Intestine Large	intestine
46	chr5:80894400-80905400	Weak transcription	Fetal Brain Female	brain
47	chr5:80894400-80905800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:80894600-80895200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr5:80894600-80895600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:80894600-80897600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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