Variant report

Variant	rs9405507
Chromosome Location	chr6:1723854-1723855
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	chr6:1610217..1612226-chr6:1723387..1726071,3	MCF-7	breast:
2	chr6:1687393..1689735-chr6:1723369..1725669,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1013064	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1022547	0.88[GIH][hapmap]
rs1022549	0.88[GIH][hapmap]
rs1022550	0.88[GIH][hapmap]
rs1986203	0.80[EUR][1000 genomes]
rs1986205	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2318106	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2318107	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4129868	1.00[AFR][1000 genomes]
rs4959150	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4959596	0.88[GIH][hapmap]
rs4959598	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4959600	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6596846	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6901836	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs6924173	0.95[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6928775	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6928953	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6937688	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6940556	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6942353	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs764518	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7746883	0.88[GIH][hapmap]
rs7754428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7754564	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7754761	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9328068	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9378308	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9378309	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9378652	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9391928	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9392325	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9392327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9392328	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9392330	1.00[CEU][hapmap]
rs9405148	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432843	chr6:1694719-1725261	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9405507	SERPINB9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
5	chr6:1704200-1725200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:1705800-1724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:1706000-1724200	Weak transcription	NHEK	skin
8	chr6:1706800-1726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:1707200-1724600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:1707800-1724600	Weak transcription	GM12878-XiMat	blood
11	chr6:1708200-1724600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:1709800-1724400	Weak transcription	Spleen	Spleen
13	chr6:1711000-1724200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:1713400-1724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:1713400-1726000	Weak transcription	Dnd41	blood
16	chr6:1715800-1724400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:1716400-1724800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:1716600-1728200	Weak transcription	Liver	Liver
20	chr6:1717000-1726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:1717600-1724200	Weak transcription	Primary T cells from cord blood	blood
22	chr6:1717600-1731600	Weak transcription	Aorta	Aorta
23	chr6:1718800-1724400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:1718800-1724600	Weak transcription	Gastric	stomach
25	chr6:1718800-1724800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:1718800-1724800	Weak transcription	Pancreas	Pancrea
27	chr6:1718800-1731400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:1719800-1725800	Weak transcription	Fetal Intestine Small	intestine
29	chr6:1721000-1724200	Weak transcription	Fetal Lung	lung
30	chr6:1721200-1731600	Weak transcription	Right Atrium	heart
31	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:1721200-1748800	Weak transcription	Osteobl	bone
33	chr6:1721400-1724200	Weak transcription	Fetal Kidney	kidney
34	chr6:1721400-1724400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:1721400-1724400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:1721400-1724400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:1721400-1724400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:1721400-1724400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:1721400-1724800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:1721400-1730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:1721400-1739400	Weak transcription	Hela-S3	cervix
42	chr6:1721600-1724000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:1721600-1724000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:1721600-1724200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:1721600-1724200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:1721600-1724600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:1721600-1726600	Weak transcription	Brain Substantia Nigra	brain
48	chr6:1721800-1724000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:1721800-1724200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:1721800-1724200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links