Variant report

Variant	rs4469007
Chromosome Location	chr3:105590533-105590534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105587379..105589688-chr3:105590274..105592993,2	K562	blood:
2	chr3:105584001..105586223-chr3:105590379..105592467,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12054270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493071	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632595	0.81[AFR][1000 genomes]
rs1443100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503923	0.98[AMR][1000 genomes]
rs16851512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16851553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16851673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851705	0.98[AMR][1000 genomes]
rs16851706	0.98[AMR][1000 genomes]
rs16851707	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120103	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2120104	0.86[ASN][1000 genomes]
rs2301028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34360428	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35909361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772517	0.88[ASN][1000 genomes]
rs3772522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821490	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs4431143	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255572	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255573	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255575	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256353	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62258160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62261460	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62261462	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62261487	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62261489	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261491	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261492	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261493	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261495	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261496	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261497	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261498	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261499	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62261538	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62261539	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62263056	0.86[ASN][1000 genomes]
rs62263057	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62263059	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62263169	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62263170	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62264260	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7619706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7628896	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7641527	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7650046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964173	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9657903	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657924	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs971109	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849559	0.86[ASN][1000 genomes]
rs9856147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105589000-105590600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:105589000-105591000	Enhancers	Fetal Heart	heart
3	chr3:105589000-105591000	Enhancers	Fetal Intestine Small	intestine
4	chr3:105589000-105595200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:105589000-105601200	Weak transcription	Aorta	Aorta
6	chr3:105589000-105601200	Weak transcription	Thymus	Thymus
7	chr3:105589000-105601200	Weak transcription	NH-A	brain
8	chr3:105589200-105590800	Enhancers	Fetal Lung	lung
9	chr3:105589200-105591000	Enhancers	Stomach Mucosa	stomach
10	chr3:105589200-105592400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:105589200-105601200	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:105589400-105594400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:105589400-105596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:105589400-105596800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:105589600-105590800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:105589600-105590800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:105589600-105594600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:105589800-105590600	Weak transcription	NHDF-Ad	bronchial
19	chr3:105589800-105590800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:105589800-105591400	Weak transcription	Osteobl	bone
21	chr3:105589800-105595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:105589800-105595400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:105589800-105595800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:105589800-105595800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:105590000-105590600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:105590000-105595600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:105590000-105595800	Weak transcription	Primary B cells from cord blood	blood
28	chr3:105590200-105590800	Enhancers	Fetal Intestine Large	intestine
29	chr3:105590200-105590800	Enhancers	Small Intestine	intestine
30	chr3:105590200-105595200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:105590200-105595200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:105590400-105592000	Weak transcription	Fetal Brain Male	brain
33	chr3:105590400-105595800	Weak transcription	Fetal Kidney	kidney

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