Variant report

Variant	rs839817
Chromosome Location	chr1:77669304-77669305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:77669001..77671084-chr1:77671530..77674115,2	MCF-7	breast:
2	chr1:77668693..77669518-chr4:102182394..102183036,2	HCT-116	colon:
3	chr1:77667810..77669464-chr1:78468632..78471293,2	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1098123	0.96[AFR][1000 genomes]
rs1098127	0.96[AFR][1000 genomes]
rs1721152	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1779167	0.94[AFR][1000 genomes]
rs1779182	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2653468	0.98[AFR][1000 genomes]
rs2653470	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2799565	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2799569	0.96[AFR][1000 genomes]
rs58815389	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs61484997	0.91[AMR][1000 genomes]
rs74090600	0.82[AFR][1000 genomes]
rs74092420	0.83[AMR][1000 genomes]
rs7546997	0.82[AFR][1000 genomes]
rs839806	0.94[AFR][1000 genomes]
rs839807	0.86[EUR][1000 genomes]
rs839811	0.96[AFR][1000 genomes]
rs839812	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs839819	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs839833	0.83[AMR][1000 genomes]
rs839837	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs839838	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs839839	0.90[AFR][1000 genomes];0.91[AMR][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	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
2	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
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77626000-77684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:77626800-77674800	Weak transcription	Ovary	ovary
3	chr1:77626800-77676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:77643400-77669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:77643600-77672600	Weak transcription	Fetal Lung	lung
6	chr1:77643800-77674400	Weak transcription	Psoas Muscle	Psoas
7	chr1:77648400-77684000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:77649000-77679800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:77649200-77672400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:77650800-77672000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:77650800-77684200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:77652600-77683400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:77653200-77670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:77654000-77669600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:77655000-77673400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:77655200-77673000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:77655200-77680400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:77655200-77684000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:77655600-77683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:77655800-77670800	Weak transcription	Dnd41	blood
21	chr1:77656400-77669800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:77656600-77669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:77657400-77680000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:77657400-77681200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:77658400-77669600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:77659200-77671000	Weak transcription	Aorta	Aorta
27	chr1:77659200-77683200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:77660800-77669400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:77660800-77672200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:77661000-77669600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:77661000-77669800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:77661000-77671000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:77661200-77669600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:77661200-77676400	Weak transcription	Left Ventricle	heart
35	chr1:77662000-77669400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:77662000-77670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:77662200-77671800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:77664200-77669600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:77666000-77679800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:77666800-77683400	Weak transcription	NHLF	lung
41	chr1:77668800-77673600	Weak transcription	Fetal Thymus	thymus
42	chr1:77669200-77669600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:77669200-77669600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:77669200-77669600	Weak transcription	Fetal Intestine Small	intestine
45	chr1:77669200-77671600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:77669200-77672400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:77669200-77672800	Weak transcription	Rectal Smooth Muscle	rectum

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