Variant report

Variant	rs4916431
Chromosome Location	chr3:196202822-196202823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196200904..196203106-chr3:196242169..196245085,2	K562	blood:

Variant related genes	Relation type
ENSG00000214097	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11185543	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707744	0.89[ASN][1000 genomes]
rs11718980	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719920	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632592	0.89[ASN][1000 genomes]
rs12635457	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13084212	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13098146	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196595	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34722299	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796129	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393941	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916497	0.90[ASN][1000 genomes]
rs4916498	0.93[ASN][1000 genomes]
rs4916499	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5016648	0.91[ASN][1000 genomes]
rs55997345	0.87[ASN][1000 genomes]
rs6772271	0.85[ASN][1000 genomes]
rs6775484	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803161	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71630192	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433483	0.89[ASN][1000 genomes]
rs7611980	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612450	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643192	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646174	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646273	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647487	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837568	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9844068	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9864836	0.91[ASN][1000 genomes]
rs9869437	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9872866	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
10	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv10389	chr3:196202319-196206791	Strong transcription Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4916431	UBXD7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196182200-196213600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:196191800-196216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:196193400-196209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:196193600-196214600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:196194200-196215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:196194200-196217400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:196194400-196211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:196194400-196216600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:196194600-196214600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:196194600-196214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:196194600-196215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:196194800-196215000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:196195000-196214800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:196195200-196215200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:196195400-196214800	Strong transcription	Liver	Liver
16	chr3:196195400-196215600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:196195600-196214400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:196195600-196215000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:196195800-196214800	Strong transcription	Dnd41	blood
20	chr3:196196000-196205400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:196196800-196207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:196196800-196208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:196196800-196214600	Strong transcription	Fetal Stomach	stomach
24	chr3:196196800-196214800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:196196800-196217000	Strong transcription	Fetal Intestine Small	intestine
26	chr3:196197000-196216800	Strong transcription	GM12878-XiMat	blood
27	chr3:196197000-196220000	Weak transcription	Stomach Mucosa	stomach
28	chr3:196197200-196214800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
30	chr3:196197400-196214600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:196197400-196214600	Strong transcription	Thymus	Thymus
32	chr3:196197600-196203800	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:196197600-196214800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:196197600-196215000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:196198200-196204800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:196198200-196205400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:196198200-196205400	Strong transcription	NH-A	brain
38	chr3:196198200-196205800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:196198200-196214800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:196198200-196215000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:196198200-196215000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:196198200-196215000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:196198400-196205400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:196198400-196214600	Strong transcription	Left Ventricle	heart
45	chr3:196198400-196215000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:196199000-196209200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:196199200-196205600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:196199200-196209800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:196199400-196209000	Weak transcription	A549	lung
50	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links