Variant report

Variant	rs17423838
Chromosome Location	chr3:111442959-111442960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12494734	0.85[YRI][hapmap]
rs13317985	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs13321524	0.81[CEU][hapmap]
rs13322494	0.81[CEU][hapmap]
rs1398753	0.90[LWK][hapmap];0.85[YRI][hapmap]
rs1398754	0.90[LWK][hapmap];0.85[YRI][hapmap]
rs17489748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292518	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs4276156	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs4381908	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4516581	0.81[CEU][hapmap]
rs56108816	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57161413	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57971051	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60844695	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66539950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762246	0.81[CEU][hapmap]
rs6762572	0.81[CEU][hapmap]
rs6782513	0.81[CEU][hapmap]
rs6787278	0.80[CEU][hapmap]
rs6789977	0.81[CEU][hapmap]
rs6790521	0.81[CEU][hapmap]
rs6790612	0.81[CEU][hapmap]
rs6790825	0.81[CEU][hapmap]
rs6790977	0.81[CEU][hapmap]
rs67923296	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795947	0.81[CEU][hapmap]
rs6800047	0.81[CEU][hapmap]
rs6800922	0.81[CEU][hapmap]
rs6802960	0.81[CEU][hapmap]
rs68057139	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7614433	0.81[CEU][hapmap]
rs9842396	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs9843288	0.81[CEU][hapmap]
rs9858064	0.81[CEU][hapmap]
rs9858228	0.81[CEU][hapmap]
rs9880633	0.81[CEU][hapmap]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111410600-111443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
3	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:111420600-111445600	Weak transcription	HepG2	liver
5	chr3:111425800-111443800	Weak transcription	Dnd41	blood
6	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
7	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:111428800-111445200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:111431600-111443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:111431600-111443800	Weak transcription	Fetal Brain Female	brain
13	chr3:111431600-111451400	Weak transcription	Gastric	stomach
14	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:111432400-111445000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:111433600-111444000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:111433800-111447000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:111434000-111443400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
22	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:111438600-111444000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:111438800-111443200	Strong transcription	Primary T cells from cord blood	blood
25	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
26	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
27	chr3:111441000-111443200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:111441000-111443400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:111441600-111443200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
34	chr3:111441800-111443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:111442000-111443000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:111442000-111443000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:111442000-111443000	Enhancers	A549	lung
38	chr3:111442000-111443000	Enhancers	NH-A	brain
39	chr3:111442000-111443200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:111442000-111443400	Enhancers	Osteobl	bone
41	chr3:111442000-111443600	Enhancers	HSMMtube	muscle
42	chr3:111442000-111443800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:111442000-111444000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
45	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:111442200-111443000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:111442200-111443000	Enhancers	Left Ventricle	heart
49	chr3:111442200-111443000	Enhancers	HMEC	breast
50	chr3:111442200-111443200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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