Variant report

Variant	rs4988342
Chromosome Location	chr17:59938736-59938737
allele	G/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59938126..59942484-chr20:52208111..52210732,4	MCF-7	breast:
2	chr17:59936062..59938856-chr20:52546755..52548819,2	MCF-7	breast:
3	chr17:59938249..59942766-chr17:60140265..60145745,10	MCF-7	breast:
4	chr17:59936074..59944748-chr20:55835834..55847370,36	MCF-7	breast:
5	chr17:59938658..59940749-chr7:99004886..99006495,2	MCF-7	breast:
6	chr17:59937475..59939110-chr20:55817376..55819720,2	MCF-7	breast:
7	chr17:59936983..59940866-chr17:60141087..60143647,5	MCF-7	breast:
8	chr17:59929026..59944759-chr20:55831267..55853908,71	MCF-7	breast:
9	chr11:62605730..62607893-chr17:59936927..59940452,3	MCF-7	breast:
10	chr17:59476206..59478986-chr17:59937418..59941494,6	MCF-7	breast:
11	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10401014	1.00[EUR][1000 genomes]
rs16945750	1.00[EUR][1000 genomes]
rs28431006	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	0.84[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs6504078	1.00[EUR][1000 genomes]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7212884	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7213026	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	1.00[EUR][1000 genomes]
rs7222876	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs7226248	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069386	0.92[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	0.85[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9892123	1.00[EUR][1000 genomes]
rs9894718	1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[EUR][1000 genomes]
rs9899780	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9902699	1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9909882	0.85[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910902	1.00[EUR][1000 genomes]
rs9913351	1.00[TSI][hapmap]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9916070	1.00[TSI][hapmap]
rs9944467	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:79 , 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	chr17:59911800-59939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:59912200-59939200	Weak transcription	HSMM	muscle
7	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:59912400-59939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:59912400-59940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:59912400-59940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:59917800-59939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:59918000-59939000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr17:59920400-59940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:59921200-59939800	Weak transcription	Thymus	Thymus
15	chr17:59921600-59940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:59922200-59939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:59923200-59939800	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:59923600-59940200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr17:59924800-59939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:59926200-59940200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr17:59926400-59939200	Weak transcription	Fetal Brain Female	brain
22	chr17:59927400-59939200	Weak transcription	Fetal Kidney	kidney
23	chr17:59927800-59938800	Weak transcription	Fetal Stomach	stomach
24	chr17:59931600-59939800	Weak transcription	Primary B cells from cord blood	blood
25	chr17:59932200-59940200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:59933400-59940400	Weak transcription	Pancreas	Pancrea
27	chr17:59933800-59938800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:59933800-59939400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:59934000-59939200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:59935000-59938800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:59935000-59939000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr17:59935000-59939000	Weak transcription	Fetal Intestine Large	intestine
33	chr17:59935000-59940200	Weak transcription	Ovary	ovary
34	chr17:59936800-59938800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:59936800-59939400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:59937000-59938800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr17:59937000-59939600	Weak transcription	Fetal Intestine Small	intestine
38	chr17:59937000-59939800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr17:59937200-59940200	Weak transcription	Small Intestine	intestine
40	chr17:59937400-59938800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:59937400-59938800	Enhancers	HepG2	liver
42	chr17:59937400-59939000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr17:59937400-59939000	Enhancers	Hela-S3	cervix
44	chr17:59937400-59939000	Weak transcription	K562	blood
45	chr17:59937600-59940200	Weak transcription	Esophagus	oesophagus
46	chr17:59937800-59938800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:59937800-59938800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr17:59937800-59938800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr17:59937800-59939000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr17:59937800-59939200	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links