Variant report

Variant	rs2084954
Chromosome Location	chr2:149014250-149014251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10206569	0.86[ASN][1000 genomes]
rs10210377	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10432369	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10928388	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10928389	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10928390	0.86[ASN][1000 genomes]
rs1120671	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11675979	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11676308	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678688	0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11683219	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11685302	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692246	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053104	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12470061	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12691780	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12691781	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13001946	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022005	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027785	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13032996	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13392141	0.86[ASN][1000 genomes]
rs13425594	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449960	0.88[EUR][1000 genomes]
rs1453318	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17274896	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869341	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2044760	0.88[EUR][1000 genomes]
rs2044761	0.87[EUR][1000 genomes]
rs2167127	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839755	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890917	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35042809	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35749985	0.84[ASN][1000 genomes]
rs4399670	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4972276	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4972277	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4972278	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4972338	0.87[EUR][1000 genomes]
rs4972341	0.86[ASN][1000 genomes]
rs4972343	0.80[ASN][1000 genomes]
rs4972347	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4972355	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6430305	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721794	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746932	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570104	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7572948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949679	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs961207	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs987625	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs987626	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs991554	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148994800-149016600	Weak transcription	Fetal Brain Male	brain
2	chr2:148995000-149019800	Weak transcription	Aorta	Aorta
3	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
4	chr2:148995400-149015200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:148999400-149016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:149002600-149015600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:149002800-149016600	Weak transcription	NHLF	lung
9	chr2:149009200-149016600	ZNF genes & repeats	GM12878-XiMat	blood
10	chr2:149009400-149017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:149009600-149017600	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr2:149010800-149014800	ZNF genes & repeats	Dnd41	blood
13	chr2:149011000-149014400	ZNF genes & repeats	Fetal Stomach	stomach
14	chr2:149011000-149017000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:149011200-149014400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr2:149011400-149016400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:149011600-149014400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr2:149011600-149017000	Strong transcription	Fetal Intestine Large	intestine
19	chr2:149011600-149017200	ZNF genes & repeats	Fetal Thymus	thymus
20	chr2:149011600-149017600	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr2:149011600-149030800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:149011800-149014600	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr2:149011800-149015400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:149011800-149016400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:149011800-149016600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:149011800-149016800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:149011800-149021200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:149012000-149017000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:149012000-149017000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:149012000-149019000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:149012200-149015800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:149012200-149016600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:149012200-149017000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:149012400-149014400	Weak transcription	Ovary	ovary
35	chr2:149012400-149015200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:149012400-149015600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:149012400-149017200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:149012600-149016600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:149012600-149043400	Weak transcription	Gastric	stomach
40	chr2:149012800-149015200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:149012800-149016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:149012800-149017000	Weak transcription	Brain Anterior Caudate	brain
43	chr2:149012800-149030000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:149012800-149030200	Weak transcription	Fetal Kidney	kidney
45	chr2:149012800-149030800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:149013000-149015400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:149013000-149015800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:149013000-149017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:149013000-149017600	Weak transcription	Right Ventricle	heart

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