Variant report

Variant	rs534069000
Chromosome Location	chr3:195975778-195975779
allele	C/T
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	SPI1	chr3:195975661-195975832	GM12878	blood:	n/a	n/a
2	SIN3AK20	chr3:195975725-195975861	HepG2	liver:	n/a	n/a
3	USF1	chr3:195975717-195975898	HepG2	liver:	n/a	n/a
4	PAX5	chr3:195975658-195975961	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195952863..195955052-chr3:195973498..195975966,2	K562	blood:

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000228028	TF binding region
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	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
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	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
8	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	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
13	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
14	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	33 gene(s)	inside rSNPs	diseases
18	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
19	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
20	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
21	esv3341217	chr3:195972755-195975953	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	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
23	esv3356671	chr3:195975455-195979753	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 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	chr3:195959600-195978200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:195962400-195977000	Strong transcription	Fetal Stomach	stomach
3	chr3:195962400-195979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:195965200-195994200	Weak transcription	A549	lung
5	chr3:195965600-195975800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:195965800-195976600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:195967200-195988600	Strong transcription	Fetal Intestine Small	intestine
9	chr3:195968400-195976400	Strong transcription	Spleen	Spleen
10	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:195969200-195978200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:195969600-195982400	Weak transcription	Fetal Heart	heart
13	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
14	chr3:195971200-195979600	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:195971600-195978400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:195971800-195976000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:195972200-195976400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:195972200-195978600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:195972200-195979000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:195972200-195979200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:195972400-195975800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:195972400-195976400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:195972400-195977200	Strong transcription	Fetal Intestine Large	intestine
24	chr3:195972400-195977800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:195972800-195976600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:195973000-195976800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
28	chr3:195974400-195988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:195974600-195975800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:195974600-195976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:195974600-195981600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:195974600-195981800	Weak transcription	Brain Germinal Matrix	brain
34	chr3:195974600-195981800	Weak transcription	Psoas Muscle	Psoas
35	chr3:195974600-195981800	Weak transcription	NHDF-Ad	bronchial
36	chr3:195974600-195982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:195974600-195983600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:195974600-195987800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:195974800-195976200	Weak transcription	Primary B cells from cord blood	blood
41	chr3:195974800-195977600	Weak transcription	Fetal Lung	lung
42	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
44	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
45	chr3:195975000-195976600	Weak transcription	GM12878-XiMat	blood
46	chr3:195975000-195977600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:195975000-195978200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:195975000-195980200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:195975000-195981000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:195975000-195981400	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links