Variant report

Variant	rs3007411
Chromosome Location	chr1:246889540-246889541
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246858802..246860634-chr1:246887473..246889819,2	MCF-7	breast:
2	chr1:246862215..246864763-chr1:246888186..246891481,3	K562	blood:
3	chr1:246884666..246886259-chr1:246889523..246891914,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127783	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10159002	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10754532	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10802442	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10924820	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10924823	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10924824	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12027222	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085330	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12090470	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12142760	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12144408	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3007316	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3007317	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007318	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007322	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007323	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007324	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34649985	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34989088	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3795463	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3795464	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130316	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4130317	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244627	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4244630	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4926454	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4926455	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4926457	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4926459	0.91[ASN][1000 genomes]
rs6426323	0.85[ASN][1000 genomes]
rs6426326	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664883	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6685364	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72764626	0.97[ASN][1000 genomes]
rs7364715	0.98[ASN][1000 genomes]
rs7365076	0.86[ASN][1000 genomes]
rs7366377	0.89[ASN][1000 genomes]
rs7416239	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526537	0.80[ASN][1000 genomes]
rs7532929	0.83[ASN][1000 genomes]
rs9426218	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426267	0.82[EUR][1000 genomes]
rs9426269	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9426271	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888000-246889800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:246888400-246889800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:246888400-246890600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:246888400-246890800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:246888400-246891000	Weak transcription	Aorta	Aorta
6	chr1:246888400-246891600	Weak transcription	Esophagus	oesophagus
7	chr1:246888400-246893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:246888400-246896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
13	chr1:246888600-246890200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:246888600-246890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:246888600-246890200	Enhancers	Placenta	Placenta
16	chr1:246888600-246890400	Weak transcription	Psoas Muscle	Psoas
17	chr1:246888600-246890600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:246888600-246890600	Flanking Active TSS	Liver	Liver
19	chr1:246888600-246890600	Enhancers	Hela-S3	cervix
20	chr1:246888600-246890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:246888600-246890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:246888600-246891400	Weak transcription	Right Ventricle	heart
23	chr1:246888600-246893400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:246888600-246901400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:246888800-246889800	Enhancers	Pancreas	Pancrea
27	chr1:246888800-246890000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:246888800-246890200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:246888800-246890200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:246888800-246890200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:246888800-246890200	Weak transcription	Primary T cells from cord blood	blood
32	chr1:246888800-246890200	Weak transcription	Left Ventricle	heart
33	chr1:246888800-246890200	Weak transcription	Thymus	Thymus
34	chr1:246888800-246890200	Weak transcription	HSMMtube	muscle
35	chr1:246888800-246890800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:246888800-246890800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:246888800-246890800	Weak transcription	Ovary	ovary
38	chr1:246888800-246891000	Weak transcription	Gastric	stomach
39	chr1:246888800-246891000	Weak transcription	Spleen	Spleen
40	chr1:246888800-246891200	Weak transcription	Lung	lung
41	chr1:246888800-246891600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:246888800-246892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:246888800-246897400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:246889000-246889600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:246889000-246889800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:246889000-246889800	Weak transcription	Brain Substantia Nigra	brain
49	chr1:246889000-246889800	Weak transcription	HSMM	muscle
50	chr1:246889000-246890000	Enhancers	Primary hematopoietic stem cells	blood

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