Variant report

Variant	rs7041802
Chromosome Location	chr9:100981757-100981758
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: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	chr9:100981625..100983478-chr9:100983956..100985664,2	MCF-7	breast:
2	chr9:100971294..100973425-chr9:100980256..100981977,2	K562	blood:
3	chr9:100967414..100970312-chr9:100980747..100984136,3	K562	blood:
4	chr9:100978764..100982569-chr9:100985493..100988173,3	K562	blood:
5	chr9:100834907..100836936-chr9:100979916..100984357,4	MCF-7	breast:
6	chr9:100981458..100983417-chr9:100991263..100992969,2	MCF-7	breast:
7	chr9:100978143..100990074-chr9:101014745..101021064,26	MCF-7	breast:
8	chr9:100979926..100982589-chr9:101013541..101016209,2	MCF-7	breast:
9	chr9:100974658..100976665-chr9:100978962..100981975,3	MCF-7	breast:
10	chr9:100981284..100982951-chr9:100985877..100987433,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10818610	0.91[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10985480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985507	0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs12348328	1.00[ASW][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes]
rs2417894	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758257	1.00[ASW][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7041802	COX7A1	trans	brain	seeQTL
rs7041802	TBC1D2	cis	cerebellum	SCAN
rs7041802	TBC1D2	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr9:100959600-100984400	Strong transcription	Osteobl	bone
4	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
6	chr9:100965600-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:100968000-100987000	Weak transcription	Small Intestine	intestine
8	chr9:100968400-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:100968600-100985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:100968800-100984600	Weak transcription	K562	blood
14	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:100969000-100984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:100969200-100985600	Strong transcription	Fetal Intestine Small	intestine
18	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
19	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:100969800-100991800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:100970000-100985400	Strong transcription	Spleen	Spleen
22	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:100970400-100983800	Strong transcription	HSMMtube	muscle
24	chr9:100971200-100981800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:100971200-100985200	Strong transcription	Lung	lung
26	chr9:100971400-100982200	Weak transcription	Ovary	ovary
27	chr9:100971400-100985400	Strong transcription	Fetal Intestine Large	intestine
28	chr9:100971600-100982000	Weak transcription	Pancreas	Pancrea
29	chr9:100972400-100983800	Strong transcription	HSMM	muscle
30	chr9:100973000-100981800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:100973000-100985800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:100973800-100985400	Weak transcription	Stomach Mucosa	stomach
33	chr9:100974000-100984800	Strong transcription	Esophagus	oesophagus
34	chr9:100974800-100985200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:100974800-101010600	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:100975200-100982400	Enhancers	Liver	Liver
37	chr9:100975200-100983800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr9:100975600-100981800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:100976400-100981800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:100976400-100982200	Weak transcription	Thymus	Thymus
41	chr9:100976400-100984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:100976400-100984400	Weak transcription	NHDF-Ad	bronchial
43	chr9:100976400-100998800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:100976600-100982200	Weak transcription	Fetal Stomach	stomach
45	chr9:100977400-100982000	Weak transcription	Left Ventricle	heart
46	chr9:100977400-100982200	Weak transcription	Aorta	Aorta
47	chr9:100977400-100982200	Weak transcription	Right Ventricle	heart
48	chr9:100978200-100984200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr9:100978200-100985200	Weak transcription	HepG2	liver
50	chr9:100978400-100984200	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links