Variant report

Variant	rs150309075
Chromosome Location	chr3:52000611-52000612
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	YY1	chr3:52000520-52000877	SK-N-SH_RA	brain:	n/a	chr3:52000711-52000730 chr3:52000718-52000728 chr3:52000717-52000725 chr3:52000706-52000728 chr3:52000712-52000729 chr3:52000719-52000727
2	YY1	chr3:52000549-52000848	SK-N-SH_RA	brain:	n/a	chr3:52000711-52000730 chr3:52000718-52000728 chr3:52000717-52000725 chr3:52000706-52000728 chr3:52000712-52000729 chr3:52000719-52000727
3	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
4	YY1	chr3:52000468-52000892	H1-hESC	embryonic stem cell:	n/a	chr3:52000711-52000730 chr3:52000718-52000728 chr3:52000717-52000725 chr3:52000706-52000728 chr3:52000712-52000729 chr3:52000719-52000727
5	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:52000308-52002203	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51996322..51998656-chr3:51999527..52001457,4	MCF-7	breast:
3	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
4	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
5	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
6	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
7	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:

Variant related genes	Relation type
ABHD14A	TF binding region
PCBP4	TF binding region
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3403794	chr3:52000337-52003085	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51990600-52000800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:51994600-52000800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:51996200-52001000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:51996600-52001200	Enhancers	Fetal Brain Male	brain
5	chr3:51996600-52001200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr3:51997800-52001200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:51998000-52000800	Enhancers	Pancreas	Pancrea
8	chr3:51998400-52000800	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr3:51998400-52000800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:51998600-52001200	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr3:51999000-52000800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr3:51999000-52000800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr3:51999000-52001200	Flanking Active TSS	Fetal Brain Female	brain
14	chr3:51999200-52000800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr3:51999200-52001000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr3:51999200-52001200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:51999200-52001200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:51999400-52000800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:51999400-52000800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
20	chr3:51999400-52000800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:51999600-52000800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:51999600-52001200	Flanking Active TSS	HepG2	liver
23	chr3:51999800-52000800	Enhancers	NHEK	skin
24	chr3:51999800-52001000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:51999800-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:51999800-52001200	Flanking Active TSS	HMEC	breast
27	chr3:51999800-52001400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:51999800-52001400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr3:52000000-52000800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
30	chr3:52000000-52000800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:52000000-52000800	Enhancers	Lung	lung
32	chr3:52000000-52001000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr3:52000000-52001000	Bivalent Enhancer	Fetal Thymus	thymus
34	chr3:52000000-52001000	Enhancers	Spleen	Spleen
35	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52000000-52001200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:52000000-52001200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:52000000-52001200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr3:52000000-52001200	Flanking Active TSS	HSMM	muscle
41	chr3:52000200-52000800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:52000200-52000800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:52000200-52000800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:52000200-52000800	Enhancers	Esophagus	oesophagus
45	chr3:52000200-52000800	Enhancers	Fetal Lung	lung
46	chr3:52000200-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:52000200-52001200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:52000200-52001200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr3:52000200-52001200	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr3:52000200-52001200	Flanking Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links