Variant report

Variant	rs4008004
Chromosome Location	chr9:15300968-15300969
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15298408..15301257-chr9:15344895..15347811,2	MCF-7	breast:
2	chr9:15300090..15302521-chr9:15304681..15306725,2	MCF-7	breast:
3	chr9:15298942..15301605-chr9:15420446..15422025,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10114494	0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10115392	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10118629	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10121612	0.83[ASN][1000 genomes]
rs10125948	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10738391	0.82[CHB][hapmap]
rs10810374	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10961963	0.82[ASN][1000 genomes]
rs10961965	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs17327373	0.94[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs491322	0.83[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv524849	chr9:15299590-15362057	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4008004	TTC39B	cis	Lymphoblastoid	GTEx
rs4008004	TTC39B	cis	lymphoblastoid	seeQTL
rs4008004	C9orf52	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:15296600-15301200	Enhancers	Primary B cells from peripheral blood	blood
7	chr9:15296800-15305600	Weak transcription	Left Ventricle	heart
8	chr9:15297000-15305200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:15297200-15305600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:15297200-15305600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:15297200-15305600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:15297400-15304800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:15297400-15305200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:15297400-15305600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:15297400-15305600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:15297400-15305600	Weak transcription	NHEK	skin
17	chr9:15297400-15305600	Weak transcription	NHLF	lung
18	chr9:15297400-15306000	Weak transcription	HSMM	muscle
19	chr9:15297600-15301000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:15297600-15301000	Strong transcription	Fetal Stomach	stomach
21	chr9:15297600-15304600	Weak transcription	Stomach Mucosa	stomach
22	chr9:15297600-15305200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:15297600-15305200	Weak transcription	HMEC	breast
24	chr9:15297600-15305400	Weak transcription	Fetal Lung	lung
25	chr9:15297600-15305400	Weak transcription	Osteobl	bone
26	chr9:15297600-15305600	Weak transcription	Adipose Nuclei	Adipose
27	chr9:15297600-15305600	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:15297600-15305600	Weak transcription	Esophagus	oesophagus
29	chr9:15297600-15305600	Weak transcription	Lung	lung
30	chr9:15297600-15305600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:15297600-15305800	Weak transcription	Gastric	stomach
32	chr9:15297600-15305800	Weak transcription	Right Atrium	heart
33	chr9:15297800-15304800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:15297800-15305600	Weak transcription	NHDF-Ad	bronchial
35	chr9:15297800-15306000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:15298000-15305400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:15298200-15305800	Weak transcription	Brain Angular Gyrus	brain
38	chr9:15298600-15305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:15299000-15305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:15299200-15301000	Strong transcription	Fetal Intestine Small	intestine
41	chr9:15299200-15304600	Weak transcription	Small Intestine	intestine
42	chr9:15299200-15305000	Weak transcription	Fetal Kidney	kidney
43	chr9:15299200-15305400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:15299400-15305200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:15299600-15304800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:15299800-15304200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:15300000-15301400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:15300000-15301400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr9:15300000-15301400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:15300000-15301600	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links