Variant report

Variant	rs4404423
Chromosome Location	chr3:42828111-42828112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42821893..42823608-chr3:42825720..42828571,2	K562	blood:
2	chr3:42825788..42828570-chr3:42866080..42867830,2	K562	blood:
3	chr3:42823433..42825988-chr3:42826908..42830376,3	MCF-7	breast:
4	chr3:42827288..42829555-chr3:42832078..42833794,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11129971	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs123506	1.00[CHB][hapmap]
rs123509	1.00[CHB][hapmap]
rs12488173	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1564176	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991438	0.82[AFR][1000 genomes]
rs339661	1.00[CHB][hapmap]
rs339663	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339682	1.00[CHB][hapmap]
rs339683	1.00[CHB][hapmap]
rs339686	1.00[CHB][hapmap]
rs35033264	1.00[MEX][hapmap]
rs35426298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs5027058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs551658	1.00[CHB][hapmap]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6763762	1.00[CHB][hapmap]
rs6773223	1.00[CHB][hapmap]
rs6773636	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773675	1.00[MEX][hapmap]
rs6777653	1.00[MEX][hapmap]
rs6778695	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798412	1.00[CHB][hapmap]
rs6802779	1.00[MEX][hapmap]
rs6865	1.00[CHB][hapmap]
rs735320	1.00[CHB][hapmap]
rs7610350	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612614	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.90[AFR][1000 genomes]
rs7641452	1.00[CHB][hapmap]
rs7648688	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311331	1.00[CHB][hapmap]
rs9755640	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9865715	1.00[CHB][hapmap]
rs9866005	0.81[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	1.00[MEX][hapmap];0.85[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	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv236207	chr3:42825586-42829088	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
2	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:42815200-42828200	Weak transcription	Fetal Intestine Small	intestine
4	chr3:42815200-42834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42815200-42834800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:42815200-42834800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:42815200-42834800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:42815200-42834800	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:42815200-42834800	Weak transcription	Ovary	ovary
10	chr3:42815200-42834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42815200-42834800	Weak transcription	A549	lung
12	chr3:42815200-42835200	Weak transcription	Right Ventricle	heart
13	chr3:42815200-42836400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:42815200-42837400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
17	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
18	chr3:42815400-42832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:42815400-42833600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:42815400-42834400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:42815400-42834800	Weak transcription	Brain Germinal Matrix	brain
22	chr3:42815400-42837200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
24	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
25	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:42816200-42837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:42820400-42834800	Weak transcription	HSMMtube	muscle
29	chr3:42821400-42828400	Strong transcription	Dnd41	blood
30	chr3:42821400-42837400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:42821800-42834800	Weak transcription	Esophagus	oesophagus
32	chr3:42821800-42834800	Weak transcription	Pancreas	Pancrea
33	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:42822400-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:42822400-42834800	Weak transcription	NHLF	lung
36	chr3:42822400-42837200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
38	chr3:42822800-42830000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:42822800-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:42822800-42837000	Weak transcription	Brain Anterior Caudate	brain
41	chr3:42822800-42841600	Weak transcription	Brain Substantia Nigra	brain
42	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
44	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:42823000-42832400	Weak transcription	Fetal Heart	heart
46	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain
47	chr3:42823600-42830200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:42823600-42831000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:42823600-42834800	Weak transcription	Colonic Mucosa	Colon
50	chr3:42823600-42836400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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