Variant report

Variant	rs13089205
Chromosome Location	chr3:196127406-196127407
allele	A/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	chr3:196127372-196127511	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196119980..196121933-chr3:196124713..196127635,2	K562	blood:

Variant related genes	Relation type
RN7SL434P	TF binding region
ENSG00000206644	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10881567	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11185537	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12488531	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12638961	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13073879	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28549737	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594421	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34702811	0.83[AFR][1000 genomes]
rs35561509	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4133244	0.82[AMR][1000 genomes]
rs4290832	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4371545	0.81[AFR][1000 genomes]
rs4513483	0.82[AFR][1000 genomes]
rs4579046	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4916428	0.83[AFR][1000 genomes]
rs6583303	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73213970	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7373049	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7373103	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7373385	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7374841	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617626	0.83[AFR][1000 genomes]
rs7624107	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821735	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839978	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841810	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847223	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860931	0.84[AFR][1000 genomes]
rs9874783	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
3	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
5	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
6	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:196115400-196127800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:196115400-196127800	Strong transcription	Placenta	Placenta
9	chr3:196115400-196127800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:196115400-196129800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:196115600-196134600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:196116200-196129200	Strong transcription	Fetal Stomach	stomach
13	chr3:196116200-196134000	Strong transcription	Fetal Intestine Small	intestine
14	chr3:196116600-196131800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:196116600-196133600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:196117800-196127800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:196117800-196131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:196118000-196133600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:196118000-196134800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:196118800-196130400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:196118800-196133600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:196118800-196136000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:196120400-196130800	Strong transcription	GM12878-XiMat	blood
25	chr3:196120400-196133600	Weak transcription	Fetal Brain Male	brain
26	chr3:196121400-196134000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr3:196121600-196127600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:196122400-196127600	Strong transcription	Thymus	Thymus
29	chr3:196122400-196128000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:196122400-196130200	Strong transcription	Fetal Intestine Large	intestine
31	chr3:196122400-196130600	Strong transcription	Fetal Thymus	thymus
32	chr3:196122400-196134200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:196123400-196128000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:196123400-196134000	Strong transcription	Primary B cells from cord blood	blood
35	chr3:196123600-196127800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:196123800-196127600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:196123800-196127800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:196123800-196127800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:196123800-196128000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:196123800-196128000	Strong transcription	Adipose Nuclei	Adipose
41	chr3:196123800-196129400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:196123800-196129600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:196123800-196129800	Strong transcription	Liver	Liver
44	chr3:196123800-196130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:196123800-196134600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:196124000-196127600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:196124000-196127600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:196124000-196127600	Strong transcription	Ovary	ovary
49	chr3:196124000-196127600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:196124000-196127800	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links