Variant report

Variant	rs3954945
Chromosome Location	chr9:3532777-3532778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3531967..3534867-chr9:3591369..3594064,2	K562	blood:
2	chr9:3470655..3472991-chr9:3531327..3534236,2	K562	blood:
3	chr9:3532189..3534806-chr9:3549602..3552356,2	K562	blood:
4	chr9:3505495..3510523-chr9:3529335..3535947,8	K562	blood:
5	chr9:3532661..3534867-chr9:3592564..3594236,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10115088	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10118702	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10758299	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10814208	0.83[ASN][1000 genomes]
rs10814219	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814233	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814235	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10814250	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10814251	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10972435	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10972438	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133463	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133467	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004862	0.83[EUR][1000 genomes]
rs12684702	0.89[ASN][1000 genomes]
rs2027089	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28510559	0.85[EUR][1000 genomes]
rs7022948	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027862	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041399	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7042747	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045092	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847562	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7858486	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7864107	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7867083	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7871094	0.83[ASN][1000 genomes]
rs7871777	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873538	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9774864	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9792451	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3954945	RP11-509J21.1	cis	Artery Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3527400-3535000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:3527400-3567600	Weak transcription	Ovary	ovary
3	chr9:3527600-3534600	Weak transcription	Pancreas	Pancrea
4	chr9:3527800-3534000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:3528000-3532800	Weak transcription	NHDF-Ad	bronchial
6	chr9:3528000-3535000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:3528000-3536000	Weak transcription	Brain Substantia Nigra	brain
8	chr9:3528000-3536200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:3528200-3541200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:3528200-3550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:3528600-3532800	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:3528600-3534400	Weak transcription	Fetal Intestine Large	intestine
13	chr9:3528600-3535000	Weak transcription	Fetal Intestine Small	intestine
14	chr9:3528600-3554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:3528800-3533000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:3528800-3533000	Weak transcription	Psoas Muscle	Psoas
17	chr9:3528800-3533600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:3528800-3534200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:3528800-3535000	Weak transcription	Small Intestine	intestine
20	chr9:3528800-3536200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:3528800-3553600	Weak transcription	Adipose Nuclei	Adipose
22	chr9:3528800-3560600	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:3529000-3533800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:3529000-3579000	Weak transcription	HSMMtube	muscle
25	chr9:3529200-3533000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr9:3529200-3533800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:3529200-3536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:3529200-3541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:3529200-3548400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:3529200-3550800	Weak transcription	Primary B cells from cord blood	blood
31	chr9:3529400-3532800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:3529400-3535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:3529400-3536200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:3529800-3548800	Weak transcription	Primary T cells from cord blood	blood
35	chr9:3530000-3556400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:3530200-3532800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:3530200-3553600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:3530800-3537400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:3531000-3532800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:3531000-3575800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:3531200-3532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:3531200-3534000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:3531200-3534600	Weak transcription	K562	blood
44	chr9:3531200-3541400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:3531200-3564600	Weak transcription	HSMM	muscle
46	chr9:3531800-3535000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:3531800-3537400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:3531800-3579000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:3532000-3536000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:3532200-3532800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links