Variant report

Variant	rs7044658
Chromosome Location	chr9:16519571-16519572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16518671..16520605-chr9:16526925..16528585,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10121584	0.82[CEU][hapmap]
rs10124761	0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10738435	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756757	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1927630	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3829848	0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs7023752	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7043485	0.87[YRI][hapmap]
rs943737	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943738	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7044658	TTC39B	cis	parietal	SCAN
rs7044658	C9orf150	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16515600-16519600	Weak transcription	Fetal Brain Male	brain
2	chr9:16515600-16522000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:16515600-16532600	Weak transcription	Aorta	Aorta
4	chr9:16516200-16521200	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:16516200-16521600	Weak transcription	HSMMtube	muscle
6	chr9:16516200-16521800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:16516200-16522000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:16516200-16522000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:16516200-16522000	Weak transcription	Left Ventricle	heart
10	chr9:16516200-16522200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:16516200-16524800	Weak transcription	Lung	lung
12	chr9:16516400-16519800	Weak transcription	Right Atrium	heart
13	chr9:16516400-16521000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:16517000-16522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:16517200-16520000	Weak transcription	NHDF-Ad	bronchial
16	chr9:16517200-16521400	Weak transcription	Brain Substantia Nigra	brain
17	chr9:16517200-16521400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:16517200-16521400	Weak transcription	HSMM	muscle
19	chr9:16517200-16522000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:16517200-16522000	Weak transcription	Fetal Thymus	thymus
21	chr9:16517200-16522000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:16517200-16526800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:16517400-16520200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:16517600-16520000	Weak transcription	Fetal Stomach	stomach
25	chr9:16517600-16521200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:16517600-16521200	Weak transcription	NH-A	brain
27	chr9:16517600-16521600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:16517600-16521800	Weak transcription	Fetal Kidney	kidney
29	chr9:16517800-16520800	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:16517800-16521400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:16517800-16521400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:16518000-16519600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:16518000-16520400	Weak transcription	Osteobl	bone
34	chr9:16518000-16521600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:16518000-16524200	Weak transcription	A549	lung
36	chr9:16518400-16520600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:16518400-16521800	Weak transcription	HUVEC	blood vessel
38	chr9:16518600-16520000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr9:16518600-16520200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr9:16518600-16520800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr9:16518800-16519600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr9:16518800-16520000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr9:16518800-16520200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr9:16518800-16520200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:16518800-16521000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:16518800-16524800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:16519000-16519600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:16519000-16519600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:16519000-16520200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:16519000-16520200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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