Variant report

Variant	rs10852940
Chromosome Location	chr17:38590706-38590707
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38588496..38590793-chr17:38771686..38774374,2	MCF-7	breast:
2	chr17:38518098..38520397-chr17:38589062..38590766,2	MCF-7	breast:
3	chr17:38580560..38584947-chr17:38585760..38591436,7	K562	blood:
4	chr17:38572288..38574196-chr17:38590587..38593029,2	K562	blood:
5	chr17:38581114..38584947-chr17:38588775..38591436,4	K562	blood:
6	chr17:38587923..38591705-chr17:38591977..38594441,3	MCF-7	breast:
7	chr17:38587525..38592353-chr17:38597530..38601586,11	MCF-7	breast:
8	chr17:38517929..38522150-chr17:38588397..38591798,3	K562	blood:
9	chr17:38588081..38591030-chr17:38591069..38592804,4	K562	blood:
10	chr17:38517929..38520889-chr17:38588435..38591798,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141753	Chromatin interaction
ENSG00000131747	Chromatin interaction
ENSG00000183153	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1009570	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078945	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11657212	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868758	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015561	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35103116	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890114	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs56394376	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584438	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584828	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598892	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632224	0.92[EUR][1000 genomes];0.99[ASN][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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38579600-38598800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:38584000-38592600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr17:38584600-38600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:38588600-38591200	Enhancers	Fetal Stomach	stomach
5	chr17:38588600-38592600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:38589000-38590800	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr17:38589200-38590800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:38589400-38590800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr17:38589400-38591200	Enhancers	Brain Germinal Matrix	brain
10	chr17:38589600-38592600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:38589600-38598800	Weak transcription	Fetal Intestine Small	intestine
12	chr17:38589800-38591200	Enhancers	Rectal Smooth Muscle	rectum
13	chr17:38589800-38593200	Weak transcription	Fetal Lung	lung
14	chr17:38589800-38598600	Weak transcription	NHDF-Ad	bronchial
15	chr17:38590000-38590800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:38590000-38591200	Enhancers	Colon Smooth Muscle	Colon
17	chr17:38590000-38593200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr17:38590000-38593400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:38590200-38590800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:38590200-38592600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr17:38590200-38593200	Weak transcription	Right Atrium	heart
22	chr17:38590200-38593400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr17:38590200-38593600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:38590200-38599000	Weak transcription	Lung	lung
25	chr17:38590400-38591200	Enhancers	Stomach Smooth Muscle	stomach
26	chr17:38590400-38593200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:38590400-38593200	Weak transcription	Spleen	Spleen
28	chr17:38590400-38593800	Weak transcription	Fetal Thymus	thymus
29	chr17:38590400-38597400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:38590400-38598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:38590400-38598800	Weak transcription	Osteobl	bone
32	chr17:38590600-38592800	Weak transcription	Fetal Muscle Leg	muscle
33	chr17:38590600-38592800	Weak transcription	K562	blood
34	chr17:38590600-38593000	Weak transcription	Left Ventricle	heart
35	chr17:38590600-38593000	Weak transcription	Right Ventricle	heart
36	chr17:38590600-38593200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr17:38590600-38593200	Weak transcription	NHLF	lung
38	chr17:38590600-38593600	Weak transcription	Placenta	Placenta
39	chr17:38590600-38596600	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links