Variant report

Variant	rs3774406
Chromosome Location	chr3:42653722-42653723
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1062051	0.89[ASN][1000 genomes]
rs13072295	0.82[ASN][1000 genomes]
rs13089845	0.81[ASN][1000 genomes]
rs13090902	0.81[ASN][1000 genomes]
rs13093680	0.82[ASN][1000 genomes]
rs17030476	1.00[EUR][1000 genomes]
rs17074662	0.89[ASN][1000 genomes]
rs17074664	0.92[ASN][1000 genomes]
rs17074669	0.92[ASN][1000 genomes]
rs17074673	0.82[ASN][1000 genomes]
rs17074674	0.82[ASN][1000 genomes]
rs17074680	0.92[ASN][1000 genomes]
rs17074693	0.89[ASN][1000 genomes]
rs17074834	1.00[EUR][1000 genomes]
rs17511541	1.00[EUR][1000 genomes]
rs2271182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2284303	0.87[ASN][1000 genomes]
rs2284304	0.82[ASN][1000 genomes]
rs2300057	0.82[ASN][1000 genomes]
rs2300058	0.82[ASN][1000 genomes]
rs2302352	0.82[ASN][1000 genomes]
rs33969824	0.89[ASN][1000 genomes]
rs339700	1.00[EUR][1000 genomes]
rs34683820	0.82[ASN][1000 genomes]
rs34687113	0.89[ASN][1000 genomes]
rs34762478	0.86[ASN][1000 genomes]
rs34801786	0.81[ASN][1000 genomes]
rs34852409	0.82[ASN][1000 genomes]
rs35506005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.81[ASN][1000 genomes]
rs35770315	0.92[ASN][1000 genomes]
rs35890296	0.82[ASN][1000 genomes]
rs36033201	0.82[ASN][1000 genomes]
rs3774401	0.89[ASN][1000 genomes]
rs3774402	0.89[ASN][1000 genomes]
rs3774404	0.89[ASN][1000 genomes]
rs3774407	0.82[ASN][1000 genomes]
rs3846058	0.89[ASN][1000 genomes]
rs3846059	0.82[ASN][1000 genomes]
rs3856737	0.82[ASN][1000 genomes]
rs3886782	0.84[ASN][1000 genomes]
rs56797870	0.82[ASN][1000 genomes]
rs57259216	0.82[ASN][1000 genomes]
rs58868911	0.82[ASN][1000 genomes]
rs59914338	0.89[ASN][1000 genomes]
rs60348477	0.86[ASN][1000 genomes]
rs61149998	0.89[ASN][1000 genomes]
rs6441928	0.82[ASN][1000 genomes]
rs66786953	0.82[ASN][1000 genomes]
rs67165547	0.82[ASN][1000 genomes]
rs67533173	0.85[ASN][1000 genomes]
rs6772312	0.82[ASN][1000 genomes]
rs6778982	0.82[ASN][1000 genomes]
rs6788548	0.82[ASN][1000 genomes]
rs6793186	0.82[ASN][1000 genomes]
rs6795296	0.82[ASN][1000 genomes]
rs68028490	0.83[ASN][1000 genomes]
rs68071013	0.89[ASN][1000 genomes]
rs72864072	0.82[ASN][1000 genomes]
rs72865703	1.00[EUR][1000 genomes]
rs7617403	0.89[ASN][1000 genomes]
rs7617736	0.89[ASN][1000 genomes]
rs7624628	0.82[ASN][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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
8	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:42644200-42655200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
12	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
13	chr3:42644800-42660200	Weak transcription	NH-A	brain
14	chr3:42645200-42660200	Weak transcription	HMEC	breast
15	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42646200-42654000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:42647000-42671400	Weak transcription	NHEK	skin
18	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:42647400-42654600	Weak transcription	Right Ventricle	heart
21	chr3:42647400-42672000	Weak transcription	NHLF	lung
22	chr3:42647600-42654600	Weak transcription	A549	lung
23	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:42647600-42677600	Weak transcription	Gastric	stomach
25	chr3:42648200-42655400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
27	chr3:42649000-42657600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:42649400-42657000	Weak transcription	Primary B cells from cord blood	blood
29	chr3:42649800-42654400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
31	chr3:42650200-42660000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:42650400-42654600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:42650400-42654600	Enhancers	Primary T cells from cord blood	blood
34	chr3:42650400-42654600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:42650400-42654600	Weak transcription	Brain Substantia Nigra	brain
36	chr3:42650400-42657400	Weak transcription	Osteobl	bone
37	chr3:42650400-42658600	Weak transcription	HSMM	muscle
38	chr3:42650400-42659800	Weak transcription	Fetal Thymus	thymus
39	chr3:42650400-42660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:42650400-42660000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:42650400-42660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:42650400-42660600	Weak transcription	Fetal Heart	heart
43	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
44	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:42650600-42657000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:42650600-42657000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:42650600-42657400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:42650600-42658200	Weak transcription	Psoas Muscle	Psoas
50	chr3:42650600-42658200	Weak transcription	Right Atrium	heart

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