Variant report

Variant	rs34705953
Chromosome Location	chr3:19997111-19997112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19996748..19999658-chr3:20007262..20009565,3	K562	blood:
2	chr3:19987480..19989660-chr3:19996323..19998191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11128927	0.88[ASN][1000 genomes]
rs11128928	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11128929	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11128930	0.87[ASN][1000 genomes]
rs11128931	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1143451	0.87[ASN][1000 genomes]
rs12629485	0.92[ASN][1000 genomes]
rs13065319	0.84[ASN][1000 genomes]
rs13076973	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077307	0.82[ASN][1000 genomes]
rs13078505	0.85[ASN][1000 genomes]
rs13082980	0.84[ASN][1000 genomes]
rs13086159	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13089853	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13097697	0.87[AFR][1000 genomes]
rs13098388	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17181400	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17181862	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17796115	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34305656	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34343204	0.87[ASN][1000 genomes]
rs34417128	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35175665	0.87[ASN][1000 genomes]
rs35713165	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4610240	0.87[AFR][1000 genomes]
rs59086970	0.84[ASN][1000 genomes]
rs59608170	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60255931	0.84[ASN][1000 genomes]
rs6796425	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs71316239	0.82[AFR][1000 genomes]
rs7615145	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618928	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7634934	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7646128	0.92[ASN][1000 genomes]
rs9877801	0.84[ASN][1000 genomes]
rs9878879	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
5	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
7	chr3:19991400-19998200	Weak transcription	Aorta	Aorta
8	chr3:19991400-19998800	Strong transcription	Fetal Thymus	thymus
9	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:19991600-19997200	Strong transcription	NH-A	brain
11	chr3:19991600-19998400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:19991600-19998400	Weak transcription	Psoas Muscle	Psoas
13	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:19991800-19997600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:19991800-19998000	Strong transcription	Fetal Intestine Large	intestine
17	chr3:19992000-19998200	Strong transcription	K562	blood
18	chr3:19992000-20000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:19992000-20000200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:19992200-19998400	Strong transcription	Placenta	Placenta
24	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
26	chr3:19992400-19997400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:19992400-19997600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:19992400-19997600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:19992400-19997800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:19992400-19997800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:19992400-19998200	Strong transcription	Osteobl	bone
32	chr3:19992400-19998400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:19992400-19998600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:19992400-19999000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:19992400-20001000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:19992600-19998400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:19992600-20000400	Strong transcription	HSMM	muscle
38	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:19992800-19998800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:19992800-19999000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:19993000-19997800	Strong transcription	Brain Anterior Caudate	brain
42	chr3:19993000-19997800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:19993200-19998800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:19993200-19999600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:19993200-20000200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:19993400-19998600	Weak transcription	Right Atrium	heart
47	chr3:19993400-19999000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:19993600-19997600	Weak transcription	Ovary	ovary
49	chr3:19993600-20000200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links