Variant report

Variant	rs4133244
Chromosome Location	chr3:196157010-196157011
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196156951-196157110	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196122393..196124913-chr3:196156464..196158992,2	K562	blood:
2	chr3:196141252..196144269-chr3:196156132..196159326,3	K562	blood:
3	chr3:196156342..196159977-chr3:196227568..196231019,3	MCF-7	breast:
4	chr3:196014434..196017243-chr3:196157002..196159307,2	K562	blood:

Variant related genes	Relation type
UBXN7-AS1	TF binding region
ENSG00000241868	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10881567	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11185537	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488531	0.83[AMR][1000 genomes]
rs12638961	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13073879	0.83[AMR][1000 genomes]
rs13089205	0.82[AMR][1000 genomes]
rs28549737	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28594421	0.83[AMR][1000 genomes]
rs35561509	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4290832	0.83[AMR][1000 genomes]
rs4579046	0.82[AMR][1000 genomes]
rs6583303	0.81[AMR][1000 genomes]
rs73213970	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7373049	0.82[AMR][1000 genomes]
rs7373103	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7373385	0.83[AMR][1000 genomes]
rs7374841	0.83[AMR][1000 genomes]
rs7624107	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9821735	0.80[AMR][1000 genomes]
rs9839978	0.83[AMR][1000 genomes]
rs9841810	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9847223	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9874783	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
9	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh 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	22 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4133244	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:196127600-196157400	Weak transcription	HUVEC	blood vessel
4	chr3:196132600-196157400	Weak transcription	Liver	Liver
5	chr3:196134200-196157400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:196134600-196157800	Weak transcription	A549	lung
7	chr3:196138200-196157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:196141600-196157400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:196141600-196158000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:196142000-196157400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:196143600-196157400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:196145800-196157400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:196147200-196157400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:196147800-196158000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:196148200-196157800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:196148600-196157400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:196149800-196158000	Weak transcription	Placenta	Placenta
18	chr3:196150200-196157400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:196150400-196157400	Weak transcription	Osteobl	bone
20	chr3:196150400-196157800	Weak transcription	NH-A	brain
21	chr3:196150400-196158200	Weak transcription	Aorta	Aorta
22	chr3:196150400-196158200	Weak transcription	Colonic Mucosa	Colon
23	chr3:196150600-196157200	Weak transcription	Pancreas	Pancrea
24	chr3:196150600-196157400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:196150600-196157400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:196150600-196157400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:196150600-196157400	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:196150600-196157400	Weak transcription	Fetal Lung	lung
29	chr3:196150600-196157400	Weak transcription	Ovary	ovary
30	chr3:196150600-196157400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:196150600-196157400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:196150600-196157400	Weak transcription	Right Atrium	heart
33	chr3:196150600-196157400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:196150600-196157400	Weak transcription	HMEC	breast
35	chr3:196150600-196157400	Weak transcription	HSMM	muscle
36	chr3:196150600-196157400	Weak transcription	HSMMtube	muscle
37	chr3:196150600-196158000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:196150600-196158000	Weak transcription	Brain Substantia Nigra	brain
39	chr3:196150600-196158000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:196150600-196158200	Weak transcription	Esophagus	oesophagus
41	chr3:196150600-196158200	Weak transcription	Gastric	stomach
42	chr3:196150600-196158200	Weak transcription	Small Intestine	intestine
43	chr3:196150600-196158200	Weak transcription	Spleen	Spleen
44	chr3:196151200-196157200	Weak transcription	Psoas Muscle	Psoas
45	chr3:196151200-196157400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:196152000-196157400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:196152200-196157600	Weak transcription	Fetal Heart	heart
48	chr3:196154000-196157800	Weak transcription	Fetal Kidney	kidney
49	chr3:196155000-196157200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:196155000-196157200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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