Variant report

Variant	rs12601453
Chromosome Location	chr17:16978691-16978692
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16973117..16976449-chr17:16977265..16979682,3	MCF-7	breast:
2	chr17:16978185..16979772-chr17:16981297..16982977,2	MCF-7	breast:
3	chr17:16972185..16973700-chr17:16976776..16979129,2	MCF-7	breast:
4	chr17:16944012..16948651-chr17:16974298..16979165,8	MCF-7	breast:
5	chr17:16978492..16979412-chr17:16990508..16991542,7	MCF-7	breast:
6	chr17:16963668..16965860-chr17:16977905..16980734,3	MCF-7	breast:
7	chr17:16978531..16979412-chr17:16990508..16991465,3	MCF-7	breast:
8	chr17:16971774..16974202-chr17:16976172..16978952,3	K562	blood:
9	chr17:16975220..16977056-chr17:16977821..16980020,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12601193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs16961340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961396	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744124	0.85[CEU][hapmap]
rs3744126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap]
rs3803762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826304	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41319048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	1.00[JPT][hapmap]
rs4328504	0.81[ASN][1000 genomes]
rs6502557	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6502565	1.00[CEU][hapmap]
rs7222600	1.00[CEU][hapmap]
rs8064771	1.00[JPT][hapmap]
rs8068857	0.84[JPT][hapmap]
rs8069241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069441	0.84[JPT][hapmap]
rs8072214	0.87[EUR][1000 genomes]
rs8076621	0.87[EUR][1000 genomes]
rs9908728	0.84[ASN][1000 genomes]
rs9909107	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
2	chr17:16954800-16981200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:16955400-16981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:16959200-16982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:16959600-16979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:16966200-16980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:16970000-16981000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:16970800-16980400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:16971000-16979000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr17:16973000-16981000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:16973000-16981200	Enhancers	Brain Anterior Caudate	brain
13	chr17:16973200-16985000	Genic enhancers	A549	lung
14	chr17:16973400-16981400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:16973600-16979800	Genic enhancers	HSMM	muscle
16	chr17:16973600-16980000	Genic enhancers	HMEC	breast
17	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:16973800-16982200	Strong transcription	Fetal Brain Female	brain
19	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr17:16974200-16979200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:16974200-16979400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:16974200-16979600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:16974200-16979600	Enhancers	Psoas Muscle	Psoas
24	chr17:16974200-16979800	Enhancers	Right Atrium	heart
25	chr17:16974200-16980000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:16974200-16980600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr17:16974200-16981200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:16974200-16981800	Genic enhancers	Fetal Intestine Large	intestine
29	chr17:16974200-16985200	Enhancers	Brain Angular Gyrus	brain
30	chr17:16974400-16979600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:16974400-16979800	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr17:16974400-16985200	Genic enhancers	Fetal Intestine Small	intestine
33	chr17:16974600-16979000	Enhancers	Fetal Thymus	thymus
34	chr17:16975200-16979200	Enhancers	Fetal Heart	heart
35	chr17:16975200-16979400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr17:16975200-16979400	Enhancers	Left Ventricle	heart
37	chr17:16975200-16979600	Genic enhancers	Placenta	Placenta
38	chr17:16975200-16979800	Genic enhancers	Fetal Stomach	stomach
39	chr17:16975400-16979400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr17:16975400-16980400	Weak transcription	HepG2	liver
41	chr17:16975800-16984600	Strong transcription	Primary B cells from cord blood	blood
42	chr17:16976000-16979000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:16976000-16981200	Enhancers	Brain Cingulate Gyrus	brain
44	chr17:16976200-16978800	Enhancers	NH-A	brain
45	chr17:16976200-16981200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr17:16976600-16979600	Enhancers	NHDF-Ad	bronchial
47	chr17:16976600-16979800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr17:16976800-16978800	Enhancers	Colonic Mucosa	Colon
49	chr17:16976800-16979000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr17:16976800-16979600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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