Variant report

Variant	rs12603878
Chromosome Location	chr17:59933996-59933997
allele	A/C
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59927825..59931202-chr17:59932161..59936802,4	K562	blood:
2	chr17:59933221..59935009-chr17:59940363..59941938,2	K562	blood:
3	chr17:59476806..59479518-chr17:59933956..59936489,2	MCF-7	breast:
4	chr17:59933212..59935530-chr17:59937646..59939783,2	K562	blood:
5	chr17:59932992..59934807-chr20:52480453..52483312,2	MCF-7	breast:
6	chr17:59933754..59935568-chr8:128878993..128881692,2	MCF-7	breast:
7	chr17:59929026..59944759-chr20:55831267..55853908,71	MCF-7	breast:
8	chr17:59932616..59934615-chr20:55850907..55852718,2	MCF-7	breast:
9	chr17:59932235..59934023-chr7:99061650..99063719,2	MCF-7	breast:
10	chr17:59713223..59715658-chr17:59933248..59936932,3	MCF-7	breast:
11	chr17:59931650..59934249-chr20:52184447..52186962,3	MCF-7	breast:
12	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10512491	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12601229	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12601523	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12603627	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12937188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs16945638	1.00[MKK][hapmap]
rs16945670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16945724	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs16945762	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1809077	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014444	0.89[CHB][hapmap]
rs2378946	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4988340	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs72843732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72843737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843746	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72843758	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843759	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843762	0.84[EUR][1000 genomes]
rs72843767	0.82[EUR][1000 genomes]
rs753765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9910451	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:59905800-59939000	Weak transcription	Primary T cells from cord blood	blood
4	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:59911600-59937800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:59911800-59939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr17:59912000-59938400	Weak transcription	HUVEC	blood vessel
8	chr17:59912200-59939200	Weak transcription	HSMM	muscle
9	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:59912400-59938600	Weak transcription	NHDF-Ad	bronchial
11	chr17:59912400-59938600	Weak transcription	NHEK	skin
12	chr17:59912400-59939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:59912400-59940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:59912400-59940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:59914600-59938600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:59916600-59938600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:59917800-59939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:59918000-59939000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr17:59919800-59934600	Weak transcription	Ovary	ovary
20	chr17:59920400-59940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:59921200-59939800	Weak transcription	Thymus	Thymus
22	chr17:59921600-59940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:59922000-59937800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:59922200-59938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:59922200-59939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:59923200-59938400	Weak transcription	Osteobl	bone
27	chr17:59923200-59939800	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:59923600-59940200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr17:59924600-59934400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:59924600-59937800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:59924800-59939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:59925600-59934800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:59926200-59940200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr17:59926400-59939200	Weak transcription	Fetal Brain Female	brain
35	chr17:59927200-59936600	Weak transcription	Fetal Intestine Small	intestine
36	chr17:59927200-59938000	Weak transcription	NHLF	lung
37	chr17:59927200-59938600	Weak transcription	Brain Germinal Matrix	brain
38	chr17:59927400-59939200	Weak transcription	Fetal Kidney	kidney
39	chr17:59927800-59938800	Weak transcription	Fetal Stomach	stomach
40	chr17:59928600-59937800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr17:59928800-59934600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr17:59928800-59935000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:59929000-59934800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:59929000-59938600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:59929600-59937400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:59931000-59935000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr17:59931200-59934000	Strong transcription	HepG2	liver
48	chr17:59931200-59934800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr17:59931400-59935000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:59931600-59939800	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links