Variant report

Variant	rs17392822
Chromosome Location	chr3:99743735-99743736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99738958..99740738-chr3:99742397..99744464,2	K562	blood:
2	chr3:99742093..99744324-chr3:99758867..99761377,2	MCF-7	breast:
3	chr3:99535676..99538284-chr3:99742285..99745121,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs16842034	1.00[EUR][1000 genomes]
rs17313676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314998	1.00[ASW][hapmap]
rs17338576	1.00[EUR][1000 genomes]
rs17393080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17397949	1.00[EUR][1000 genomes]
rs17584271	1.00[ASW][hapmap]
rs17779605	1.00[EUR][1000 genomes]
rs2035400	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs36005744	1.00[EUR][1000 genomes]
rs41444055	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs41477051	0.89[AFR][1000 genomes]
rs6762809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6762871	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6764470	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6765822	0.89[AFR][1000 genomes]
rs6768684	1.00[EUR][1000 genomes]
rs6772519	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6778756	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6781780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6784150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787184	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6788807	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789840	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6790187	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6791426	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6794130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6801514	1.00[YRI][hapmap]
rs6805703	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6805834	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6807137	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6807615	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs72936590	0.83[EUR][1000 genomes]
rs7611313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7626214	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7628458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637974	1.00[YRI][hapmap]
rs7646221	1.00[EUR][1000 genomes]
rs7648943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652596	1.00[EUR][1000 genomes]
rs766777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs768527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:99725000-99745600	Weak transcription	Left Ventricle	heart
5	chr3:99726400-99748200	Weak transcription	HSMM	muscle
6	chr3:99727000-99746400	Weak transcription	Right Atrium	heart
7	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:99728800-99746200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:99733800-99745800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:99735600-99750400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:99738400-99744400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:99739200-99743800	Enhancers	Adipose Nuclei	Adipose
13	chr3:99739800-99744800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:99741000-99744200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:99741000-99744200	Enhancers	Pancreas	Pancrea
16	chr3:99741000-99744800	Enhancers	Psoas Muscle	Psoas
17	chr3:99741200-99743800	Enhancers	HMEC	breast
18	chr3:99741200-99744400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:99741200-99744600	Enhancers	NH-A	brain
20	chr3:99741200-99744600	Enhancers	Osteobl	bone
21	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
22	chr3:99741400-99744400	Enhancers	HepG2	liver
23	chr3:99741400-99744800	Enhancers	NHDF-Ad	bronchial
24	chr3:99741600-99744200	Enhancers	Small Intestine	intestine
25	chr3:99741600-99744400	Enhancers	Fetal Intestine Large	intestine
26	chr3:99741600-99744800	Enhancers	Ovary	ovary
27	chr3:99741800-99744200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:99741800-99744200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:99741800-99744200	Enhancers	Esophagus	oesophagus
30	chr3:99741800-99744600	Enhancers	Fetal Intestine Small	intestine
31	chr3:99741800-99745200	Enhancers	Stomach Mucosa	stomach
32	chr3:99742000-99744200	Enhancers	Fetal Kidney	kidney
33	chr3:99742200-99745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:99742200-99751000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
36	chr3:99742600-99749200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:99742800-99744800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:99742800-99745200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:99743000-99743800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:99743000-99750800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:99743200-99744000	Enhancers	Rectal Smooth Muscle	rectum
42	chr3:99743200-99744200	Enhancers	Duodenum Mucosa	Duodenum
43	chr3:99743400-99743800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:99743400-99744000	Enhancers	Stomach Smooth Muscle	stomach
45	chr3:99743400-99744200	Enhancers	Liver	Liver
46	chr3:99743600-99743800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:99743600-99743800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:99743600-99743800	Enhancers	Brain Hippocampus Middle	brain
49	chr3:99743600-99743800	Enhancers	A549	lung
50	chr3:99743600-99743800	Enhancers	HUVEC	blood vessel

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