Variant report

Variant	rs7800262
Chromosome Location	chr7:140025908-140025909
allele	C/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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:159133078..159133848-chr7:140025763..140026547,2	MCF-7	breast:
2	chr7:139758879..139760781-chr7:140025827..140028156,2	K562	blood:
3	chr7:139875682..139878782-chr7:140024340..140026416,3	K562	blood:
4	chr7:139761220..139765061-chr7:140022436..140026098,3	K562	blood:
5	chr7:139874264..139875531-chr7:140025860..140026775,5	K562	blood:
6	chr7:139705358..139706253-chr7:140025500..140026651,4	K562	blood:
7	chr3:13503033..13503787-chr7:140025782..140026717,2	MCF-7	breast:
8	chr7:139778501..139779573-chr7:140025840..140026699,4	MCF-7	breast:
9	chr7:140024951..140026986-chr7:140033594..140036380,2	K562	blood:
10	chr7:139705364..139706338-chr7:140025755..140026704,5	MCF-7	breast:
11	chr7:139769866..139772271-chr7:140024148..140026188,2	K562	blood:
12	chr17:46230814..46231633-chr7:140025800..140026385,2	MCF-7	breast:
13	chr7:139929869..139932027-chr7:140025336..140027515,3	MCF-7	breast:
14	chr7:139703443..139703966-chr7:140025822..140026642,2	MCF-7	breast:
15	chr7:139874914..139875818-chr7:140025450..140026669,4	MCF-7	breast:
16	chr7:139778539..139779438-chr7:140025787..140026371,2	MCF-7	breast:
17	chr7:139875688..139878782-chr7:140020537..140027140,7	K562	blood:
18	chr7:139997065..139997701-chr7:140025856..140026716,5	MCF-7	breast:
19	chr7:140024572..140026122-chr7:140027015..140029639,2	K562	blood:
20	chr7:140024916..140027848-chr7:140096767..140099113,2	K562	blood:
21	chr7:140019180..140022735-chr7:140023014..140025983,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000157800	Chromatin interaction
ENSG00000260231	Chromatin interaction
ENSG00000006459	Chromatin interaction
ENSG00000059378	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10952639	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12533908	0.89[CHB][hapmap]
rs12669023	0.92[ASN][1000 genomes]
rs4476922	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952512	0.82[AMR][1000 genomes]
rs6952838	0.89[CHB][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap]
rs6956771	0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs7776930	0.83[AMR][1000 genomes]
rs7790724	0.83[AMR][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	nsv889247	chr7:139855216-140033631	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1026255	chr7:139944473-140043299	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7800262	FLJ40852	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140016200-140026000	Weak transcription	Fetal Kidney	kidney
2	chr7:140016200-140034000	Weak transcription	Pancreas	Pancrea
3	chr7:140016800-140034200	Weak transcription	Small Intestine	intestine
4	chr7:140017000-140033200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:140017200-140032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:140017600-140033600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:140017600-140034000	Weak transcription	HMEC	breast
8	chr7:140018200-140026000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:140022800-140026000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:140022800-140030400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:140023600-140026000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:140023800-140033800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:140024000-140048800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:140024800-140026600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr7:140025600-140026000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:140025600-140026000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:140025600-140026000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:140025600-140026000	Enhancers	Gastric	stomach
19	chr7:140025600-140026000	Enhancers	Psoas Muscle	Psoas
20	chr7:140025600-140026000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr7:140025600-140026200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:140025600-140026200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr7:140025600-140026200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr7:140025600-140026200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:140025600-140026200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:140025600-140026200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:140025600-140026200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr7:140025600-140026200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr7:140025600-140026200	Enhancers	Fetal Intestine Large	intestine
30	chr7:140025600-140026200	Enhancers	Fetal Intestine Small	intestine
31	chr7:140025600-140026200	Enhancers	Placenta	Placenta
32	chr7:140025600-140026200	Enhancers	Right Ventricle	heart
33	chr7:140025600-140026200	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr7:140025600-140026200	Enhancers	Spleen	Spleen
35	chr7:140025600-140026200	Enhancers	Dnd41	blood
36	chr7:140025600-140026200	Flanking Active TSS	K562	blood
37	chr7:140025600-140026200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr7:140025600-140026400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr7:140025600-140026400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:140025600-140026400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:140025600-140026400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:140025600-140026400	Enhancers	Right Atrium	heart
43	chr7:140025600-140026600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:140025600-140026600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:140025600-140026600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:140025600-140026600	Enhancers	Stomach Mucosa	stomach
47	chr7:140025600-140026600	Flanking Active TSS	HepG2	liver
48	chr7:140025800-140026000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:140025800-140026000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr7:140025800-140026000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links