Variant report

Variant	rs35962164
Chromosome Location	chr9:137003441-137003442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:137003273-137004552	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:137003230-137003710	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:137003180-137003744	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:137003027-137004048	K562	blood:	n/a	n/a
5	POLR2A	chr9:137003435-137003697	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:137003378-137003503	K562	blood:	n/a	n/a
7	WRNIP1	chr9:137003398-137003576	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:137003302-137003496	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:137003222-137003999	SK-N-MC	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:41236712..41238651-chr9:137001241..137003469,2	MCF-7	breast:
2	chr9:137001564..137003951-chr9:137325246..137326831,2	MCF-7	breast:
3	chr9:136932690..136935080-chr9:137003441..137005032,2	MCF-7	breast:
4	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
5	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
6	chr9:136888792..136891646-chr9:137000403..137003499,3	MCF-7	breast:
7	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273249	TF binding region
WDR5	TF binding region
ENSG00000235106	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000221676	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs28377785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28399690	1.00[AFR][1000 genomes]
rs28421319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28425680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434714	1.00[EUR][1000 genomes]
rs28436125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28452481	1.00[AFR][1000 genomes]
rs28488634	1.00[EUR][1000 genomes]
rs28538491	1.00[EUR][1000 genomes]
rs28540578	1.00[EUR][1000 genomes]
rs28562287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28562957	1.00[AFR][1000 genomes]
rs28565058	1.00[EUR][1000 genomes]
rs28585632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28593202	1.00[EUR][1000 genomes]
rs28594106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595141	1.00[EUR][1000 genomes]
rs28626085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626885	1.00[EUR][1000 genomes]
rs28637300	1.00[EUR][1000 genomes]
rs28654988	1.00[EUR][1000 genomes]
rs28657441	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673958	1.00[EUR][1000 genomes]
rs28687115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687158	0.96[EUR][1000 genomes]
rs28701738	1.00[EUR][1000 genomes]
rs28705949	1.00[EUR][1000 genomes]
rs28708401	1.00[AFR][1000 genomes]
rs28715994	1.00[EUR][1000 genomes]
rs28733640	1.00[EUR][1000 genomes]
rs28756160	1.00[EUR][1000 genomes]
rs28759300	1.00[EUR][1000 genomes]
rs34022301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34031108	1.00[EUR][1000 genomes]
rs34062061	1.00[EUR][1000 genomes]
rs34169579	1.00[EUR][1000 genomes]
rs34194763	1.00[AFR][1000 genomes]
rs34259931	0.89[EUR][1000 genomes]
rs34350861	1.00[EUR][1000 genomes]
rs34515929	1.00[EUR][1000 genomes]
rs34523253	1.00[EUR][1000 genomes]
rs34546899	1.00[AFR][1000 genomes]
rs34856382	1.00[EUR][1000 genomes]
rs34929179	1.00[AFR][1000 genomes]
rs35158191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35237188	1.00[EUR][1000 genomes]
rs35370793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35420166	1.00[EUR][1000 genomes]
rs35504753	1.00[AFR][1000 genomes]
rs35511305	1.00[AFR][1000 genomes]
rs35874066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35924689	1.00[AFR][1000 genomes]
rs35985804	0.92[EUR][1000 genomes]
rs36029182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71483222	1.00[AFR][1000 genomes]
rs71505283	1.00[AFR][1000 genomes]
rs71505284	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137001600-137004600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:137001800-137003800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr9:137001800-137004400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:137002000-137004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:137002200-137004200	Enhancers	Fetal Heart	heart
6	chr9:137002200-137004400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:137002400-137003600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:137002400-137003600	Weak transcription	Aorta	Aorta
9	chr9:137002400-137003600	Enhancers	Fetal Lung	lung
10	chr9:137002400-137003800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:137002400-137003800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:137002400-137003800	Enhancers	Primary B cells from peripheral blood	blood
13	chr9:137002400-137003800	Enhancers	Fetal Brain Male	brain
14	chr9:137002400-137003800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:137002400-137003800	Enhancers	Placenta	Placenta
16	chr9:137002400-137003800	Enhancers	Fetal Thymus	thymus
17	chr9:137002400-137003800	Enhancers	Stomach Mucosa	stomach
18	chr9:137002400-137003800	Flanking Active TSS	HepG2	liver
19	chr9:137002400-137004000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr9:137002400-137004200	Enhancers	Gastric	stomach
21	chr9:137002400-137004200	Enhancers	Lung	lung
22	chr9:137002400-137004400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:137002400-137004400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr9:137002400-137004400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:137002400-137004400	Enhancers	Small Intestine	intestine
26	chr9:137002400-137004600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr9:137002400-137004600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:137002400-137004600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr9:137002400-137004600	Enhancers	Esophagus	oesophagus
30	chr9:137002400-137004600	Enhancers	Ovary	ovary
31	chr9:137002400-137004600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr9:137002400-137004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:137002400-137004800	Enhancers	Adipose Nuclei	Adipose
34	chr9:137002400-137004800	Enhancers	Left Ventricle	heart
35	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr9:137002600-137003600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:137002600-137003600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr9:137002600-137003600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:137002600-137003600	Enhancers	Primary B cells from cord blood	blood
42	chr9:137002600-137003600	Genic enhancers	Primary hematopoietic stem cells	blood
43	chr9:137002600-137003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:137002600-137003600	Weak transcription	NH-A	brain
45	chr9:137002600-137003600	Enhancers	Osteobl	bone
46	chr9:137002600-137003800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr9:137002600-137003800	Enhancers	Rectal Smooth Muscle	rectum
48	chr9:137002600-137004000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr9:137002600-137004000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr9:137002600-137004000	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links