Variant report

Variant	rs2009602
Chromosome Location	chr3:69121641-69121642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69103145..69105538-chr3:69119692..69122647,2	K562	blood:
2	chr3:69101278..69103420-chr3:69119745..69122521,2	MCF-7	breast:
3	chr3:69120698..69123415-chr3:69132362..69134206,2	K562	blood:
4	chr3:69103862..69105538-chr3:69119692..69122200,2	K562	blood:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction
ENSG00000144747	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10489	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1051901	0.81[CHB][hapmap]
rs11128107	0.84[TSI][hapmap]
rs13063094	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13090606	0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13099820	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271118	0.81[CHB][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2271120	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2271122	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279936	0.90[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2292198	0.81[ASN][1000 genomes]
rs2292199	0.83[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35718539	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755717	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755721	0.81[ASN][1000 genomes]
rs3772979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772980	0.81[CHB][hapmap]
rs3796213	0.81[CHB][hapmap]
rs3821562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3853157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56156415	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58950441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549162	0.80[EUR][1000 genomes]
rs6549165	0.84[TSI][hapmap]
rs6549181	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6549184	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6775065	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775256	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6777032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782474	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787569	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6807701	0.86[EUR][1000 genomes]
rs714300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611878	0.84[TSI][hapmap]
rs7615341	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7625579	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9813514	0.94[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826616	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101400-69127000	Weak transcription	Small Intestine	intestine
2	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
3	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:69102200-69127200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:69108400-69128200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:69110200-69127000	Weak transcription	Hela-S3	cervix
8	chr3:69110400-69122000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:69110600-69127000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:69110600-69127600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:69110600-69128200	Weak transcription	Right Ventricle	heart
12	chr3:69110600-69128400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:69110600-69128400	Weak transcription	Gastric	stomach
14	chr3:69110600-69128400	Weak transcription	Psoas Muscle	Psoas
15	chr3:69110800-69127000	Weak transcription	Pancreas	Pancrea
16	chr3:69110800-69127600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:69110800-69127800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:69110800-69128600	Weak transcription	Esophagus	oesophagus
19	chr3:69110800-69128800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:69110800-69128800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:69111000-69128600	Weak transcription	Lung	lung
22	chr3:69111000-69128800	Weak transcription	Spleen	Spleen
23	chr3:69111200-69121800	Weak transcription	Brain Anterior Caudate	brain
24	chr3:69111200-69128000	Weak transcription	K562	blood
25	chr3:69111200-69128200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:69111200-69128200	Weak transcription	Colonic Mucosa	Colon
27	chr3:69111400-69121800	Weak transcription	Fetal Heart	heart
28	chr3:69111400-69122200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:69111400-69127000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:69111400-69128400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:69111600-69121800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:69111600-69128200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:69111800-69126800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:69111800-69128200	Weak transcription	A549	lung
35	chr3:69112200-69121800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:69112200-69122400	Weak transcription	HMEC	breast
37	chr3:69112200-69128200	Weak transcription	Fetal Kidney	kidney
38	chr3:69112600-69121800	Weak transcription	Brain Germinal Matrix	brain
39	chr3:69112600-69123000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:69112600-69128200	Weak transcription	Fetal Brain Female	brain
41	chr3:69112600-69128200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:69113000-69128200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:69113400-69127400	Weak transcription	Fetal Lung	lung
44	chr3:69115000-69126800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:69115000-69127800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:69115000-69128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:69115400-69126400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:69115600-69122000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:69115600-69122000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:69115600-69126800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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