Variant report

Variant	rs9859073
Chromosome Location	chr3:179066854-179066855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:179065009..179066943-chr3:179078070..179080733,2	K562	blood:
2	chr3:179039334..179043117-chr3:179061578..179071936,16	MCF-7	breast:
3	chr3:179064557..179067034-chr3:179115322..179117988,2	MCF-7	breast:
4	chr3:179063838..179066998-chr3:179279826..179282991,3	K562	blood:
5	chr3:179040254..179044115-chr3:179063916..179068626,6	K562	blood:
6	chr3:178787639..178789990-chr3:179064273..179066880,2	MCF-7	breast:
7	chr3:179039679..179043417-chr3:179063023..179066951,5	K562	blood:
8	chr3:179040252..179043387-chr3:179064355..179067344,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136518	Chromatin interaction
ENSG00000242539	Chromatin interaction
ENSG00000172667	Chromatin interaction
ENSG00000269728	Chromatin interaction
ENSG00000171109	Chromatin interaction
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13318726	1.00[AMR][1000 genomes]
rs28576521	1.00[AMR][1000 genomes]
rs60118786	0.81[AFR][1000 genomes]
rs6807219	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73045118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7617958	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638761	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7639279	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9824102	1.00[AMR][1000 genomes]
rs9840736	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9847361	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850163	1.00[AMR][1000 genomes]
rs9872894	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 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	chr3:179064000-179067000	Active TSS	GM12878-XiMat	blood
2	chr3:179066000-179067000	Flanking Active TSS	Dnd41	blood
3	chr3:179066200-179067000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:179066200-179067400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:179066200-179071800	Weak transcription	Spleen	Spleen
6	chr3:179066200-179077400	Weak transcription	Small Intestine	intestine
7	chr3:179066200-179083800	Weak transcription	Aorta	Aorta
8	chr3:179066400-179067000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:179066400-179067000	Enhancers	Fetal Lung	lung
10	chr3:179066400-179067000	Weak transcription	Fetal Thymus	thymus
11	chr3:179066400-179067000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:179066400-179067000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:179066400-179067200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:179066400-179067200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:179066400-179067200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:179066400-179067200	Enhancers	Fetal Intestine Small	intestine
17	chr3:179066400-179067200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:179066400-179067200	Weak transcription	Left Ventricle	heart
19	chr3:179066400-179067400	Weak transcription	Ovary	ovary
20	chr3:179066400-179067800	Weak transcription	Placenta	Placenta
21	chr3:179066400-179068000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:179066400-179068200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:179066400-179069000	Weak transcription	Esophagus	oesophagus
24	chr3:179066400-179070000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:179066400-179070000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:179066400-179071400	Weak transcription	Lung	lung
27	chr3:179066400-179072600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:179066400-179073000	Weak transcription	Pancreas	Pancrea
29	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:179066600-179067000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:179066600-179067200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:179066600-179067200	Enhancers	Primary T cells from cord blood	blood
33	chr3:179066600-179067200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:179066600-179067200	Enhancers	Adipose Nuclei	Adipose
35	chr3:179066600-179067200	Enhancers	Fetal Intestine Large	intestine
36	chr3:179066600-179067200	Transcr. at gene 5' and 3'	K562	blood
37	chr3:179066600-179067400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:179066600-179067400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:179066600-179067400	Enhancers	Thymus	Thymus
40	chr3:179066600-179069200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:179066600-179070200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:179066600-179071200	Weak transcription	A549	lung
43	chr3:179066600-179071400	Weak transcription	Right Ventricle	heart
44	chr3:179066800-179067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:179066800-179067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:179066800-179067000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:179066800-179067000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:179066800-179067000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:179066800-179067000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
50	chr3:179066800-179067000	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links