Variant report

Variant	rs2906973
Chromosome Location	chr17:15369693-15369694
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15354358..15356547-chr17:15369300..15371690,2	K562	blood:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1019092	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10432020	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1548679	0.97[EUR][1000 genomes]
rs1548680	0.97[EUR][1000 genomes]
rs17842195	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2108757	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs2190914	0.97[EUR][1000 genomes]
rs2323734	0.97[EUR][1000 genomes]
rs2875140	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2906977	0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2906978	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2906979	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes]
rs2906980	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2906982	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2906983	0.97[EUR][1000 genomes]
rs2906984	0.97[EUR][1000 genomes]
rs2906985	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs2954759	0.85[JPT][hapmap]
rs2954761	0.86[JPT][hapmap]
rs2954765	0.81[AMR][1000 genomes]
rs2954770	0.97[EUR][1000 genomes]
rs2954771	1.00[CEU][hapmap];0.84[JPT][hapmap];0.97[EUR][1000 genomes]
rs2954772	0.97[EUR][1000 genomes]
rs2954773	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2954774	0.97[EUR][1000 genomes]
rs2954775	0.97[EUR][1000 genomes]
rs2954776	0.97[EUR][1000 genomes]
rs2954777	0.97[EUR][1000 genomes]
rs2954778	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs2954779	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56055931	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs728854	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs729355	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs729356	0.97[EUR][1000 genomes]
rs729357	0.97[EUR][1000 genomes]
rs887033	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs887034	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[EUR][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	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription 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	34 gene(s)	inside rSNPs	diseases
7	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking 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	55 gene(s)	inside rSNPs	diseases
8	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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	33 gene(s)	inside rSNPs	diseases
9	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3392219	chr17:15366827-15370125	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3441277	chr17:15367127-15370125	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:15341400-15375800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:15356800-15378000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:15357800-15375800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
6	chr17:15359400-15386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr17:15359600-15383000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:15361200-15387800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:15361400-15385400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:15361600-15373200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:15361800-15382000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:15366000-15369800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr17:15366200-15370400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:15366400-15369800	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:15367200-15371000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr17:15367400-15371400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:15367400-15372800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:15367400-15394200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:15367600-15372000	Weak transcription	Osteobl	bone
20	chr17:15367800-15370400	Weak transcription	Fetal Intestine Small	intestine
21	chr17:15367800-15375800	Weak transcription	Small Intestine	intestine
22	chr17:15368000-15370800	Weak transcription	Placenta	Placenta
23	chr17:15368000-15371000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:15368000-15373800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:15368000-15382800	Weak transcription	Hela-S3	cervix
26	chr17:15368000-15393600	Weak transcription	Aorta	Aorta
27	chr17:15368200-15378800	Weak transcription	Psoas Muscle	Psoas
28	chr17:15368200-15379000	Weak transcription	A549	lung
29	chr17:15368200-15386800	Weak transcription	Ovary	ovary
30	chr17:15368400-15372800	Weak transcription	HUVEC	blood vessel
31	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:15368600-15371000	Weak transcription	Left Ventricle	heart
33	chr17:15368600-15371000	Weak transcription	Right Atrium	heart
34	chr17:15368600-15371400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:15368600-15371400	Weak transcription	Adipose Nuclei	Adipose
36	chr17:15368600-15372800	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:15368600-15379200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr17:15368600-15385600	Weak transcription	Fetal Brain Female	brain
39	chr17:15368800-15370600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:15368800-15370800	Weak transcription	Colon Smooth Muscle	Colon
41	chr17:15368800-15371000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr17:15368800-15371000	Weak transcription	Right Ventricle	heart
43	chr17:15368800-15372400	Weak transcription	HSMM	muscle
44	chr17:15368800-15372600	Weak transcription	HepG2	liver
45	chr17:15368800-15376200	Weak transcription	Fetal Lung	lung
46	chr17:15368800-15382400	Weak transcription	Spleen	Spleen
47	chr17:15368800-15394000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:15369000-15369800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:15369000-15369800	Genic enhancers	Fetal Stomach	stomach
50	chr17:15369000-15371600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links