Variant report

Variant	rs13090152
Chromosome Location	chr3:196360161-196360162
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	POLR2A	chr3:196358486-196362153	NB4	blood:	n/a	n/a
2	POLR2A	chr3:196358490-196360955	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:196358362-196360222	HL-60	blood:	n/a	n/a
4	PML	chr3:196358337-196360191	GM12878	blood:	n/a	n/a
5	SPI1	chr3:196359705-196360165	HL-60	blood:	n/a	chr3:196359900-196359907
6	POLR2A	chr3:196358547-196361460	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:196358388-196361043	PBDE	blood:	n/a	n/a
8	POLR2A	chr3:196358282-196361457	GM12891	blood:	n/a	n/a
9	RUNX3	chr3:196358748-196360193	GM12878	blood:	n/a	chr3:196359721-196359736
10	POLR2A	chr3:196358871-196360223	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:196358527-196360185	K562	blood:	n/a	n/a
12	HCFC1	chr3:196358335-196360218	Hela-S3	cervix:	n/a	n/a
13	REST	chr3:196358479-196360200	H1-neurons	neurons:	n/a	chr3:196359501-196359514 chr3:196358946-196358964
14	REST	chr3:196358616-196360177	HL-60	blood:	n/a	chr3:196359501-196359514 chr3:196358946-196358964
15	POLR2A	chr3:196358386-196360252	K562	blood:	n/a	n/a
16	SIN3AK20	chr3:196358820-196360251	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:196358279-196360221	HL-60	blood:	n/a	n/a
18	POLR2A	chr3:196357959-196360240	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196357928..196360475-chr3:196466661..196469415,2	MCF-7	breast:
2	chr3:196359722..196361449-chr3:196369958..196371504,2	MCF-7	breast:
3	chr14:30396875..30399384-chr3:196359205..196361217,2	MCF-7	breast:
4	chr3:196293733..196296360-chr3:196359092..196361282,2	MCF-7	breast:
5	chr3:196312738..196315414-chr3:196359776..196362202,2	K562	blood:

Variant related genes	Relation type
LINC01063	TF binding region
ENSG00000185798	Chromatin interaction
ENSG00000184304	Chromatin interaction
ENSG00000180370	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1684468	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	35 gene(s)	inside rSNPs	diseases
9	nsv1003135	chr3:196348721-196738953	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196358400-196360200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:196358400-196360200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:196358400-196360200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr3:196358400-196360200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:196358600-196360200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:196358600-196360200	Active TSS	Colonic Mucosa	Colon
7	chr3:196358600-196360200	Active TSS	Fetal Kidney	kidney
8	chr3:196358600-196360200	Active TSS	Right Atrium	heart
9	chr3:196358600-196360400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:196358800-196360200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:196358800-196360400	Active TSS	Thymus	Thymus
12	chr3:196359000-196360200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:196359000-196360200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:196359000-196360200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:196359000-196360200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:196359000-196360200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:196359000-196360200	Active TSS	Brain Substantia Nigra	brain
18	chr3:196359000-196360200	Active TSS	Colon Smooth Muscle	Colon
19	chr3:196359000-196360200	Active TSS	Fetal Brain Female	brain
20	chr3:196359000-196360200	Active TSS	Fetal Intestine Large	intestine
21	chr3:196359000-196360200	Active TSS	Right Ventricle	heart
22	chr3:196359000-196360200	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr3:196359000-196360400	Active TSS	K562	blood
24	chr3:196359200-196360200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:196359200-196360200	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr3:196359200-196360200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:196359200-196360200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:196359200-196360200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:196359200-196360200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:196359200-196360200	Active TSS	Brain Angular Gyrus	brain
31	chr3:196359200-196360200	Active TSS	Brain Hippocampus Middle	brain
32	chr3:196359200-196360200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:196359200-196360200	Weak transcription	Fetal Heart	heart
34	chr3:196359200-196360200	Active TSS	Fetal Stomach	stomach
35	chr3:196359200-196360200	Active TSS	HSMM	muscle
36	chr3:196359200-196360200	Active TSS	NHLF	lung
37	chr3:196359200-196360200	Active TSS	Osteobl	bone
38	chr3:196359200-196360400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr3:196359200-196360400	Active TSS	Primary T cells from cord blood	blood
40	chr3:196359200-196360400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:196359200-196360400	Active TSS	Dnd41	blood
42	chr3:196359200-196360600	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr3:196359200-196360800	Active TSS	Rectal Smooth Muscle	rectum
44	chr3:196359400-196360800	Enhancers	Fetal Brain Male	brain
45	chr3:196359600-196360200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:196359600-196360200	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr3:196359600-196362200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:196359800-196360200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:196359800-196360200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:196359800-196360200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links