Variant report

Variant	rs839833
Chromosome Location	chr1:77619762-77619763
allele	C/T
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:29)

rs_ID	r²[population]
rs1098123	0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1098124	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1098127	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11162308	1.00[CEU][hapmap]
rs1721152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1779167	0.82[YRI][hapmap]
rs1779182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2177430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653468	0.95[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs2653470	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2799565	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2799569	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58815389	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61484997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090599	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090600	1.00[EUR][1000 genomes]
rs74092420	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7546997	0.82[YRI][hapmap]
rs839806	0.82[YRI][hapmap]
rs839807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs839811	0.82[YRI][hapmap]
rs839812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs839817	0.83[AMR][1000 genomes]
rs839819	1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839820	1.00[MEX][hapmap];0.84[YRI][hapmap]
rs839821	1.00[MEX][hapmap];0.91[YRI][hapmap]
rs839837	1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs839838	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839839	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77586400-77620600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:77592200-77623600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:77595400-77640400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:77597200-77624200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:77601000-77623600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:77604400-77623600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:77606200-77651600	Weak transcription	Aorta	Aorta
8	chr1:77609800-77628800	Weak transcription	Colonic Mucosa	Colon
9	chr1:77610000-77624800	Weak transcription	Left Ventricle	heart
10	chr1:77610400-77620800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:77611600-77620200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:77611600-77624800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:77612800-77630200	Weak transcription	Psoas Muscle	Psoas
14	chr1:77614400-77619800	Weak transcription	Brain Anterior Caudate	brain
15	chr1:77614400-77623200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:77614400-77624600	Weak transcription	Ovary	ovary
17	chr1:77614400-77624800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:77614400-77630200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:77614400-77631000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:77614400-77634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:77614400-77634000	Weak transcription	Osteobl	bone
22	chr1:77614400-77635600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:77614400-77635600	Weak transcription	NHDF-Ad	bronchial
24	chr1:77614600-77625000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:77614600-77625600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:77614600-77629600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:77614600-77632000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:77614800-77624000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:77615000-77623200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:77615000-77625200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:77615200-77625600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:77615400-77625600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:77615600-77619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:77615600-77623400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:77616200-77663200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:77616600-77624000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:77617000-77625400	Weak transcription	Adipose Nuclei	Adipose
38	chr1:77617200-77636000	Weak transcription	HSMM	muscle
39	chr1:77618000-77624600	Weak transcription	Fetal Thymus	thymus
40	chr1:77618000-77624800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:77618000-77624800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:77618200-77623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:77618200-77633000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:77618400-77624200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:77618400-77624200	Weak transcription	Dnd41	blood
46	chr1:77618400-77625000	Weak transcription	Fetal Intestine Large	intestine
47	chr1:77618400-77632200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:77618400-77633200	Weak transcription	Fetal Brain Male	brain
49	chr1:77618600-77624800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:77618600-77630000	Weak transcription	Rectal Mucosa Donor 29	rectum

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