Variant report

Variant	rs55978866
Chromosome Location	chr3:99929476-99929477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16842137	1.00[AMR][1000 genomes]
rs403858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55721822	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56186146	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56227134	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56678433	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58283662	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58869093	1.00[AMR][1000 genomes]
rs58953554	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59674041	1.00[AMR][1000 genomes]
rs62636639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6441136	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6441243	1.00[AMR][1000 genomes]
rs6783067	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6788019	1.00[AMR][1000 genomes]
rs6788854	1.00[AMR][1000 genomes]
rs6788875	1.00[AMR][1000 genomes]
rs73859916	1.00[AMR][1000 genomes]
rs73859919	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859921	1.00[AMR][1000 genomes]
rs73859924	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859925	0.80[AFR][1000 genomes]
rs73859931	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862419	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862437	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862440	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862445	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862453	1.00[AMR][1000 genomes]
rs7652753	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99917800-99933000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:99926800-99931000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:99928000-99929800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:99928000-99930000	Enhancers	Psoas Muscle	Psoas
5	chr3:99928000-99930600	Enhancers	Fetal Muscle Leg	muscle
6	chr3:99928000-99930600	Enhancers	Small Intestine	intestine
7	chr3:99928000-99930800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:99928000-99931200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr3:99928200-99931000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:99928400-99930800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:99928400-99931200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:99928600-99929800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:99928600-99929800	Enhancers	Primary T cells from cord blood	blood
14	chr3:99928600-99929800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:99928600-99929800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:99928600-99929800	Enhancers	Fetal Thymus	thymus
17	chr3:99928600-99929800	Enhancers	Right Ventricle	heart
18	chr3:99928600-99929800	Enhancers	Dnd41	blood
19	chr3:99928600-99930000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:99928600-99930000	Enhancers	Fetal Intestine Small	intestine
21	chr3:99928600-99930000	Enhancers	HepG2	liver
22	chr3:99928600-99930200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:99928600-99930200	Enhancers	Fetal Intestine Large	intestine
24	chr3:99928600-99930400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:99928600-99930400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:99928600-99930600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:99928800-99929600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:99928800-99929600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr3:99928800-99929600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:99928800-99929600	Enhancers	Aorta	Aorta
31	chr3:99928800-99929600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr3:99928800-99929600	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr3:99928800-99929600	Flanking Active TSS	NHDF-Ad	bronchial
34	chr3:99928800-99929600	Flanking Active TSS	NHLF	lung
35	chr3:99928800-99929800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:99928800-99929800	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:99928800-99929800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr3:99928800-99929800	Enhancers	Right Atrium	heart
39	chr3:99928800-99930200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:99928800-99930200	Enhancers	Stomach Mucosa	stomach
41	chr3:99928800-99930600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:99928800-99930600	Enhancers	Fetal Stomach	stomach
43	chr3:99928800-99930600	Enhancers	Ovary	ovary
44	chr3:99928800-99930800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr3:99929000-99929600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr3:99929000-99929600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr3:99929000-99929600	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr3:99929000-99929600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:99929000-99929800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:99929000-99929800	Enhancers	Brain Hippocampus Middle	brain

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