Variant report

Variant	rs10399885
Chromosome Location	chr1:120534806-120534807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10923928	0.89[ASW][hapmap];0.90[YRI][hapmap]
rs12071853	0.89[YRI][hapmap]
rs12083843	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs12087913	0.88[YRI][hapmap]
rs7523642	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs7533978	1.00[ASW][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120491200-120538800	Weak transcription	Fetal Brain Male	brain
2	chr1:120509800-120557600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:120510200-120538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:120510200-120552200	Weak transcription	HUVEC	blood vessel
5	chr1:120510800-120557400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:120511600-120557800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:120512400-120543600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:120514400-120543400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:120514400-120549400	Weak transcription	Gastric	stomach
10	chr1:120521200-120549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:120523800-120546800	Weak transcription	Esophagus	oesophagus
12	chr1:120524400-120543600	Weak transcription	Spleen	Spleen
13	chr1:120525600-120557800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:120527600-120550000	Weak transcription	Lung	lung
15	chr1:120527800-120542400	Weak transcription	Brain Germinal Matrix	brain
16	chr1:120527800-120558200	Weak transcription	Brain Angular Gyrus	brain
17	chr1:120529600-120543600	Weak transcription	Fetal Intestine Large	intestine
18	chr1:120529800-120539400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:120529800-120549400	Weak transcription	Pancreas	Pancrea
20	chr1:120529800-120557800	Weak transcription	Left Ventricle	heart
21	chr1:120530000-120541000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:120530000-120543600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:120530400-120535200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:120530400-120543800	Weak transcription	Placenta	Placenta
25	chr1:120531400-120536800	Weak transcription	Thymus	Thymus
26	chr1:120531600-120539200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:120531600-120556800	Weak transcription	Fetal Thymus	thymus
28	chr1:120531800-120538800	Weak transcription	Primary B cells from cord blood	blood
29	chr1:120531800-120538800	Weak transcription	Small Intestine	intestine
30	chr1:120531800-120543600	Weak transcription	Psoas Muscle	Psoas
31	chr1:120531800-120549600	Weak transcription	Hela-S3	cervix
32	chr1:120532000-120538800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:120532800-120538800	Weak transcription	Right Atrium	heart
34	chr1:120533000-120542400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:120533000-120555200	Weak transcription	Aorta	Aorta
36	chr1:120533000-120556800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:120533200-120535200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:120533200-120537600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:120533200-120539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:120533200-120542200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:120533200-120542400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:120533200-120558400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:120533400-120535200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:120533400-120535400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:120533400-120536200	Weak transcription	Liver	Liver
46	chr1:120533400-120536800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:120533400-120536800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:120533400-120536800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:120533400-120536800	Weak transcription	Brain Substantia Nigra	brain
50	chr1:120533400-120537600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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