Variant report

Variant	rs16830173
Chromosome Location	chr2:152390250-152390251
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	IRF1	chr2:152390160-152390356	K562	blood:	n/a	chr2:152390287-152390297 chr2:152390283-152390297 chr2:152390286-152390300 chr2:152390286-152390299 chr2:152390286-152390299
2	IRF1	chr2:152390172-152390413	K562	blood:	n/a	chr2:152390287-152390297 chr2:152390283-152390297 chr2:152390286-152390300 chr2:152390286-152390299 chr2:152390286-152390299

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152389412..152391698-chr2:152393142..152395709,2	MCF-7	breast:

Variant related genes	Relation type
NEB	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12612539	1.00[EUR][1000 genomes]
rs12612655	1.00[EUR][1000 genomes]
rs12619249	1.00[EUR][1000 genomes]
rs12621850	1.00[EUR][1000 genomes]
rs12623646	1.00[EUR][1000 genomes]
rs13413290	1.00[EUR][1000 genomes]
rs16830087	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830088	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830140	1.00[EUR][1000 genomes]
rs16830170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830174	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830189	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830216	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830236	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3213817	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35967764	1.00[EUR][1000 genomes]
rs41525550	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6730990	1.00[EUR][1000 genomes]
rs73004033	1.00[ASN][1000 genomes]
rs73004051	1.00[EUR][1000 genomes]
rs73004053	1.00[EUR][1000 genomes]
rs7569133	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv933869	chr2:152308156-152391576	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	esv1793381	chr2:152370040-152463631	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv10198	chr2:152370068-152463644	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152341600-152390600	Weak transcription	Left Ventricle	heart
2	chr2:152343200-152422200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:152348800-152400800	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:152358600-152394000	Weak transcription	Spleen	Spleen
5	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:152363200-152391800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:152370400-152403600	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:152371400-152421000	Weak transcription	Pancreas	Pancrea
10	chr2:152377200-152391800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:152377400-152393800	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:152378400-152390600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:152381000-152398000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:152381000-152410200	Weak transcription	Placenta	Placenta
15	chr2:152382800-152394000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:152383200-152392200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:152383200-152424000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:152383400-152396400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:152385800-152426800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:152387600-152390600	Weak transcription	Psoas Muscle	Psoas
21	chr2:152389000-152399200	Weak transcription	Ovary	ovary
22	chr2:152389200-152393800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:152389600-152394800	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:152389800-152412000	Strong transcription	HSMMtube	muscle
25	chr2:152390000-152391000	Strong transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links