Variant report

Variant	rs9874939
Chromosome Location	chr3:52143504-52143505
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52143099..52144932-chr3:52156866..52159747,2	MCF-7	breast:
2	chr3:52142908..52145897-chr3:52147537..52149613,3	K562	blood:
3	chr3:52135638..52138438-chr3:52142187..52143836,2	K562	blood:
4	chr3:52119415..52123026-chr3:52140546..52143765,3	K562	blood:
5	chr3:52131272..52134200-chr3:52142689..52145200,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12495536	0.82[EUR][1000 genomes]
rs12496447	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12629791	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2334961	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28387060	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2878438	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs352152	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687607	0.86[EUR][1000 genomes]
rs4687805	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687810	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773704	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777340	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6778442	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6786592	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs731684	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs735768	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs747343	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749995	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644325	0.81[EUR][1000 genomes]
rs893055	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828327	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9851576	0.86[EUR][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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
3	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:52128600-52157000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:52129200-52155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:52132200-52146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:52132200-52155200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52132400-52143600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52133200-52143600	Weak transcription	HUVEC	blood vessel
10	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:52133400-52143800	Weak transcription	Stomach Mucosa	stomach
12	chr3:52133400-52144600	Weak transcription	Gastric	stomach
13	chr3:52133400-52155000	Weak transcription	Osteobl	bone
14	chr3:52136600-52153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52136800-52144200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:52136800-52154400	Weak transcription	Hela-S3	cervix
17	chr3:52136800-52155000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:52136800-52156000	Weak transcription	A549	lung
19	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:52137200-52152400	Weak transcription	GM12878-XiMat	blood
21	chr3:52137600-52146600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:52138200-52153800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:52138800-52149400	Strong transcription	Thymus	Thymus
24	chr3:52139600-52143600	Weak transcription	Fetal Intestine Large	intestine
25	chr3:52139600-52144800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:52139600-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:52139600-52154600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:52139800-52153800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:52140400-52178200	Strong transcription	Dnd41	blood
30	chr3:52140600-52147400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:52140600-52160800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:52140800-52155000	Weak transcription	Primary T cells from cord blood	blood
33	chr3:52141000-52144200	Enhancers	Fetal Muscle Leg	muscle
34	chr3:52141200-52145400	Enhancers	Fetal Brain Male	brain
35	chr3:52141400-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:52141400-52154800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:52141600-52143600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:52141600-52145800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:52141800-52144400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:52142000-52145000	Enhancers	Adipose Nuclei	Adipose
41	chr3:52142000-52145400	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:52142000-52145400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52142000-52145400	Enhancers	Left Ventricle	heart
44	chr3:52142200-52144200	Enhancers	Fetal Muscle Trunk	muscle
45	chr3:52142200-52144600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:52142200-52144800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:52142200-52144800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:52142200-52145400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:52142200-52148600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:52142400-52143800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links