Variant report

Variant	rs59766308
Chromosome Location	chr1:224375484-224375485
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	chr1:224375301-224375626	GM12878	blood:	n/a	n/a
2	MXI1	chr1:224375388-224375524	GM12878	blood:	n/a	n/a
3	TBP	chr1:224375438-224375507	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:224369367..224372466-chr1:224374660..224377497,3	MCF-7	breast:
2	chr1:224368636..224372565-chr1:224373050..224376148,4	MCF-7	breast:
3	chr1:224374669..224377400-chr1:224391823..224393961,2	K562	blood:

Variant related genes	Relation type
DEGS1	TF binding region
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs58828252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60998173	0.85[AMR][1000 genomes]
rs73126432	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372200-224377200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr1:224372200-224377400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:224372200-224377400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:224372400-224375800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:224372400-224377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:224372400-224379600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:224372400-224380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:224372400-224381000	Weak transcription	HSMMtube	muscle
9	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
10	chr1:224372600-224377400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:224372600-224377400	Weak transcription	NH-A	brain
12	chr1:224372600-224379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:224372600-224379600	Weak transcription	HMEC	breast
14	chr1:224372600-224380000	Weak transcription	Thymus	Thymus
15	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:224372600-224392400	Weak transcription	Ovary	ovary
17	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:224372800-224376000	Strong transcription	Fetal Intestine Small	intestine
19	chr1:224372800-224380000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:224372800-224380000	Weak transcription	HSMM	muscle
21	chr1:224372800-224381000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:224373200-224375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:224373200-224376000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:224373200-224376000	Strong transcription	Fetal Stomach	stomach
27	chr1:224373200-224376000	Strong transcription	Osteobl	bone
28	chr1:224373200-224377000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:224373200-224377200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:224373200-224377400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:224373200-224377400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:224373200-224377600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:224373200-224380200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:224373200-224380200	Weak transcription	HUVEC	blood vessel
35	chr1:224373200-224380400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:224373200-224382000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
38	chr1:224373400-224375600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:224373400-224376000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:224373400-224378200	Strong transcription	A549	lung
41	chr1:224373400-224379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:224373400-224379600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:224373400-224381200	Weak transcription	Aorta	Aorta
44	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine
45	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
46	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
49	chr1:224373600-224377200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:224373600-224377400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links