Variant report

Variant	rs4405884
Chromosome Location	chr3:43288353-43288354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43281582..43285022-chr3:43286584..43289819,3	K562	blood:
2	chr3:43287138..43289386-chr3:43291194..43294036,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10212591	0.83[AFR][1000 genomes]
rs11129997	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11129998	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130003	0.80[YRI][hapmap]
rs1120779	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11713302	1.00[AMR][1000 genomes]
rs12632805	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1320157	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1320159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1395373	1.00[MEX][hapmap]
rs1472807	0.82[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs1506618	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs1996496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2036616	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs2135510	1.00[AMR][1000 genomes]
rs2372353	1.00[AMR][1000 genomes]
rs2372357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2372358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2372359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2888311	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234427	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4339089	1.00[AMR][1000 genomes]
rs4346523	0.82[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs4420837	1.00[AMR][1000 genomes]
rs4425230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4470482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4569634	0.82[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs4642093	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682681	0.82[ASW][hapmap];1.00[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682684	1.00[AMR][1000 genomes]
rs4682884	0.82[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs4682889	1.00[AMR][1000 genomes]
rs4683365	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6441771	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs6442145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6766825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6767741	1.00[AMR][1000 genomes]
rs6775392	0.82[ASW][hapmap];0.84[LWK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs6784075	1.00[AMR][1000 genomes]
rs6791682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6793755	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7616072	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7632743	0.82[ASW][hapmap]
rs7636644	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648023	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7651091	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs906156	0.82[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs906157	0.82[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs906158	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs937827	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs9755005	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs984345	1.00[AMR][1000 genomes]
rs9859465	0.84[AFR][1000 genomes];1.00[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	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43284200-43289800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr3:43284400-43288400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:43284400-43289800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:43284400-43290000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:43284400-43290000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:43284400-43290400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:43284400-43300400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:43284600-43289400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:43284600-43290000	Enhancers	Primary T cells from cord blood	blood
10	chr3:43284800-43289400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:43285000-43289600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:43285000-43289600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:43285200-43290000	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:43285400-43290000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:43285600-43290800	Enhancers	Adipose Nuclei	Adipose
16	chr3:43285800-43288400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:43285800-43289200	Weak transcription	Lung	lung
18	chr3:43285800-43298400	Weak transcription	Left Ventricle	heart
19	chr3:43286000-43289600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:43286000-43289800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:43286200-43290000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:43286800-43289000	Weak transcription	Right Atrium	heart
23	chr3:43287000-43289800	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:43287200-43290000	Enhancers	Thymus	Thymus
25	chr3:43287600-43290400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:43287800-43288400	Enhancers	Spleen	Spleen
27	chr3:43287800-43290000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:43287800-43290400	Enhancers	Brain Hippocampus Middle	brain
29	chr3:43287800-43290400	Enhancers	Fetal Muscle Leg	muscle
30	chr3:43288000-43288600	Flanking Active TSS	HUVEC	blood vessel
31	chr3:43288000-43288800	Enhancers	Brain Anterior Caudate	brain
32	chr3:43288000-43289200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:43288000-43289200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:43288000-43289400	Enhancers	Fetal Thymus	thymus
35	chr3:43288000-43289800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:43288000-43290000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:43288000-43290000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:43288200-43288400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:43288200-43288400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr3:43288200-43288400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:43288200-43288400	Enhancers	Psoas Muscle	Psoas
42	chr3:43288200-43289000	Enhancers	Small Intestine	intestine
43	chr3:43288200-43290000	Enhancers	Fetal Stomach	stomach
44	chr3:43288200-43290800	Enhancers	Stomach Smooth Muscle	stomach

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