Variant report

Variant	rs2799565
Chromosome Location	chr1:77686156-77686157
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154027	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1098124	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11162308	1.00[CEU][hapmap]
rs1721152	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1779182	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2177430	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes]
rs2653468	0.82[YRI][hapmap]
rs2653470	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs58815389	0.91[AMR][1000 genomes]
rs61484997	0.91[AMR][1000 genomes]
rs74090599	0.83[AMR][1000 genomes]
rs74092420	1.00[AMR][1000 genomes]
rs839807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839812	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839817	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs839819	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes]
rs839820	0.84[YRI][hapmap]
rs839821	0.91[YRI][hapmap]
rs839833	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs839837	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes]
rs839838	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs839839	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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77682800-77686400	Active TSS	GM12878-XiMat	blood
2	chr1:77683600-77686200	Active TSS	K562	blood
3	chr1:77683800-77686200	Active TSS	A549	lung
4	chr1:77684000-77686200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:77684000-77686200	Active TSS	NHDF-Ad	bronchial
8	chr1:77684000-77686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:77684200-77686200	Active TSS	HMEC	breast
10	chr1:77684200-77686400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:77684200-77686400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:77684400-77686200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:77684600-77686200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:77684600-77686800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:77685200-77687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:77685200-77687800	Weak transcription	Spleen	Spleen
17	chr1:77685400-77686200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr1:77685400-77688000	Weak transcription	Gastric	stomach
19	chr1:77685400-77689600	Weak transcription	Esophagus	oesophagus
20	chr1:77685600-77686200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:77685600-77686200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:77685600-77686200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:77685600-77686200	Flanking Active TSS	Osteobl	bone
24	chr1:77685600-77686400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:77685600-77686600	Flanking Active TSS	Dnd41	blood
26	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
27	chr1:77685800-77686200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:77685800-77686200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:77685800-77686200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:77685800-77686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:77685800-77686600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:77685800-77686600	Enhancers	Liver	Liver
33	chr1:77685800-77686600	Weak transcription	Hela-S3	cervix
34	chr1:77685800-77686600	Flanking Active TSS	HUVEC	blood vessel
35	chr1:77685800-77686800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:77685800-77687600	Weak transcription	Fetal Stomach	stomach
37	chr1:77685800-77687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:77685800-77687800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:77685800-77687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:77685800-77687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:77685800-77687800	Weak transcription	Aorta	Aorta
42	chr1:77685800-77688400	Weak transcription	Right Atrium	heart
43	chr1:77685800-77688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:77685800-77688600	Weak transcription	Fetal Thymus	thymus
45	chr1:77685800-77688600	Weak transcription	Psoas Muscle	Psoas
46	chr1:77685800-77688800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:77685800-77689000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:77685800-77689600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:77685800-77689600	Weak transcription	Ovary	ovary
50	chr1:77685800-77690000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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