Variant report

Variant	rs619429
Chromosome Location	chr9:79111675-79111676
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1057406	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs1085341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869782	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs11144923	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11144926	0.81[AFR][1000 genomes]
rs11144929	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1969980	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2282683	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs2476940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745555	0.95[CHB][hapmap]
rs496253	0.83[ASN][1000 genomes]
rs503222	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553806	0.86[ASN][1000 genomes]
rs553927	0.86[ASN][1000 genomes]
rs566470	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570212	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs587111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587171	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590666	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631887	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs634064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664013	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs707739	0.80[JPT][hapmap]
rs785927	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs619429	RFK	cis	parietal	SCAN
rs619429	ANXA1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
2	chr9:79080800-79117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:79081800-79117200	Weak transcription	Gastric	stomach
4	chr9:79082600-79117600	Weak transcription	NHLF	lung
5	chr9:79087600-79117400	Weak transcription	Colonic Mucosa	Colon
6	chr9:79089000-79116400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
8	chr9:79093600-79117200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:79093800-79116600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:79093800-79117000	Weak transcription	HMEC	breast
11	chr9:79093800-79118000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:79094200-79120200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:79097200-79117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:79101200-79116400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:79103800-79117200	Weak transcription	Lung	lung
16	chr9:79103800-79117800	Weak transcription	Thymus	Thymus
17	chr9:79104200-79117400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:79104400-79117400	Weak transcription	Small Intestine	intestine
19	chr9:79104600-79117600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:79105800-79117200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr9:79106200-79117200	Weak transcription	HUVEC	blood vessel
22	chr9:79106600-79115000	Weak transcription	Stomach Mucosa	stomach
23	chr9:79107000-79116600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:79107600-79116400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:79108000-79117200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:79108200-79117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:79108400-79114400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:79108800-79117200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:79109000-79113000	Strong transcription	Osteobl	bone
30	chr9:79109000-79115400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:79109200-79117200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:79109200-79117200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:79109400-79113800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:79109400-79117200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr9:79109400-79117200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:79110000-79112400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:79110200-79116200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:79110400-79112000	Strong transcription	HSMM	muscle
39	chr9:79110400-79117400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:79110600-79111800	Strong transcription	Fetal Intestine Small	intestine
41	chr9:79110600-79113400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:79110600-79117000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr9:79110800-79112600	Strong transcription	Primary B cells from cord blood	blood
44	chr9:79110800-79113200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:79110800-79116600	Weak transcription	GM12878-XiMat	blood
46	chr9:79111200-79113600	Enhancers	HepG2	liver
47	chr9:79111200-79116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:79111200-79116400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr9:79111400-79111800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr9:79111400-79112400	Strong transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links