Variant report

Variant	rs17616543
Chromosome Location	chr17:38270067-38270068
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38214362..38216887-chr17:38268670..38271173,2	K562	blood:
2	chr17:38267755..38271453-chr17:38442988..38446987,5	K562	blood:
3	chr17:38268196..38271117-chr17:38323045..38325430,4	MCF-7	breast:
4	chr17:38268213..38270113-chr17:38284781..38287108,2	MCF-7	breast:
5	chr17:38269583..38271786-chr17:38337084..38338600,2	MCF-7	breast:
6	chr17:38269014..38270098-chr17:38324705..38325344,4	MCF-7	breast:
7	chr17:38220464..38222269-chr17:38268473..38270990,2	MCF-7	breast:
8	chr17:38269477..38271026-chr17:38303126..38305486,2	MCF-7	breast:
9	chr17:38267480..38272193-chr17:38332816..38336625,5	MCF-7	breast:
10	chr17:38268818..38270189-chr17:38347742..38348733,4	K562	blood:
11	chr17:38267838..38274115-chr17:38331817..38337587,12	MCF-7	breast:
12	chr17:38269526..38271162-chr17:38374700..38377094,2	MCF-7	breast:
13	chr17:38269557..38271189-chr17:38326632..38328200,2	MCF-7	breast:
14	chr17:38248607..38250140-chr17:38268958..38271761,2	K562	blood:
15	chr17:7386961..7387663-chr17:38269432..38270188,2	Hela-S3	cervix:
16	chr17:38268792..38270376-chr17:80055353..80057881,2	MCF-7	breast:
17	chr17:38247453..38250107-chr17:38269665..38271761,2	K562	blood:
18	chr17:38269551..38272040-chr17:38476568..38478805,2	MCF-7	breast:
19	chr17:38269490..38271710-chr17:38295731..38297283,2	K562	blood:
20	chr17:38180489..38185018-chr17:38268156..38272012,4	MCF-7	breast:
21	chr17:38267549..38271045-chr17:38302108..38305053,4	MCF-7	breast:
22	chr17:38168576..38170277-chr17:38268230..38270228,2	K562	blood:
23	chr17:38269604..38271663-chr17:38319802..38322582,2	MCF-7	breast:
24	chr17:38268889..38271750-chr17:38296269..38298064,2	MCF-7	breast:
25	chr17:38224965..38226879-chr17:38268479..38270883,2	MCF-7	breast:
26	chr17:38269045..38271015-chr17:38309924..38312531,2	MCF-7	breast:
27	chr17:38136359..38138448-chr17:38268198..38270997,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108352	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000169710	Chromatin interaction
ENSG00000126351	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000171475	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000094804	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10512482	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1104761	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12103533	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs15685	1.00[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965669	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965734	0.92[EUR][1000 genomes]
rs16965736	0.92[EUR][1000 genomes]
rs17616365	1.00[AMR][1000 genomes]
rs17616672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616879	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678817	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678959	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679086	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28526298	0.92[EUR][1000 genomes]
rs33998939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35783632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35898909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41283417	0.92[EUR][1000 genomes]
rs41283423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45612441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214783	0.85[EUR][1000 genomes]
rs8067519	0.92[EUR][1000 genomes]
rs8071687	0.92[EUR][1000 genomes]
rs8077482	0.92[EUR][1000 genomes]
rs9889905	0.92[EUR][1000 genomes]
rs9891944	1.00[EUR][1000 genomes]
rs9894364	0.92[EUR][1000 genomes]
rs9894807	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9898500	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9899425	0.92[EUR][1000 genomes]
rs9900154	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9903293	0.92[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9909777	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9910373	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9915775	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908221	chr17:38216522-38289003	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv528369	chr17:38256693-38289003	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38262200-38270400	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr17:38263400-38272400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:38264000-38270400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:38266200-38270400	Enhancers	Spleen	Spleen
5	chr17:38266400-38270400	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr17:38266400-38270600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:38266400-38270600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr17:38266600-38270400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr17:38266800-38271200	Flanking Active TSS	HepG2	liver
10	chr17:38267200-38271000	Flanking Active TSS	Osteobl	bone
11	chr17:38267800-38271000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:38268200-38270400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr17:38268200-38271000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:38268400-38270400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr17:38269000-38270400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr17:38269000-38270400	Flanking Active TSS	Dnd41	blood
17	chr17:38269000-38270600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:38269200-38270200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr17:38269200-38270200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr17:38269200-38270400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:38269200-38271400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:38269400-38270200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr17:38269400-38270200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr17:38269400-38270200	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr17:38269400-38270400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr17:38269400-38270400	Flanking Active TSS	Fetal Kidney	kidney
27	chr17:38269400-38270400	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr17:38269600-38270200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr17:38269600-38270200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr17:38269600-38270200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:38269600-38270200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr17:38269600-38270200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr17:38269600-38270200	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr17:38269600-38270200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr17:38269600-38270200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr17:38269600-38270200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr17:38269600-38270200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:38269600-38270200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr17:38269600-38270200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr17:38269600-38270200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:38269600-38270200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr17:38269600-38270200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:38269600-38270200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:38269600-38270200	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr17:38269600-38270200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr17:38269600-38270200	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr17:38269600-38270200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr17:38269600-38270200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr17:38269600-38270200	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr17:38269600-38270200	Flanking Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links