Variant report

Variant	rs56054779
Chromosome Location	chr2:233640871-233640872
allele	G/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	TCF7L2	chr2:233640791-233641384	HEK293	kidney:	n/a	n/a
2	GATA3	chr2:233640853-233641760	MCF-7	breast:	n/a	chr2:233640989-233641000 chr2:233641681-233641691

No.	Distal block	Cell Line	Cell type
1	chr2:233640072..233641665-chr2:233646228..233648024,2	K562	blood:
2	chr1:198125307..198127521-chr2:233640176..233642520,2	MCF-7	breast:
3	chr2:233627414..233629760-chr2:233639796..233641450,2	MCF-7	breast:
4	chr2:233635753..233637631-chr2:233640086..233642797,2	K562	blood:

Variant related genes	Relation type
GIGYF2	TF binding region
KCNJ13	TF binding region
ENSG00000204120	Chromatin interaction
ENSG00000252452	Chromatin interaction
ENSG00000151414	Chromatin interaction
ENSG00000115474	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10176930	0.84[ASN][1000 genomes]
rs10190211	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207739	0.88[ASN][1000 genomes]
rs10209575	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10933407	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10933408	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679581	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684636	0.88[ASN][1000 genomes]
rs11685169	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687379	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11688622	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11688691	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11689661	0.88[ASN][1000 genomes]
rs11694434	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11695762	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052869	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12694915	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694916	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12988087	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13386650	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13396293	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13401578	0.94[ASN][1000 genomes]
rs13408229	0.88[ASN][1000 genomes]
rs13412034	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13412513	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13425525	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429857	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1446307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293782	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305139	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491817	0.83[EUR][1000 genomes]
rs34063802	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34832091	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35778045	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35785837	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35928329	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41266951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62193305	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6747479	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73005582	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7557131	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7564554	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9288675	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9808146	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973586	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:233611600-233645600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:233612000-233644600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:233614600-233643600	Weak transcription	Small Intestine	intestine
6	chr2:233621400-233644400	Strong transcription	Liver	Liver
7	chr2:233627800-233645000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:233628600-233644200	Weak transcription	Ovary	ovary
9	chr2:233628600-233655400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:233629200-233655800	Weak transcription	Colonic Mucosa	Colon
11	chr2:233629400-233642000	Weak transcription	Gastric	stomach
12	chr2:233629400-233644200	Weak transcription	Right Ventricle	heart
13	chr2:233629400-233649600	Weak transcription	Spleen	Spleen
14	chr2:233629400-233652600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:233629400-233655200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:233629400-233655400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:233630800-233641000	Weak transcription	Fetal Kidney	kidney
18	chr2:233630800-233641200	Weak transcription	Brain Anterior Caudate	brain
19	chr2:233631600-233659200	Weak transcription	Psoas Muscle	Psoas
20	chr2:233633400-233641000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:233633400-233652600	Weak transcription	Brain Germinal Matrix	brain
22	chr2:233633600-233649600	Weak transcription	Pancreas	Pancrea
23	chr2:233634000-233641000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:233634000-233643400	Weak transcription	Fetal Heart	heart
25	chr2:233635600-233643200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:233636000-233642000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:233636200-233641000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:233636200-233641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:233636200-233641200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:233636200-233641200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:233636200-233643200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:233636200-233643600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:233636200-233644200	Weak transcription	HMEC	breast
34	chr2:233636200-233646200	Weak transcription	HSMMtube	muscle
35	chr2:233636200-233646400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:233636200-233646400	Weak transcription	K562	blood
37	chr2:233636200-233649600	Weak transcription	Aorta	Aorta
38	chr2:233636200-233649600	Weak transcription	Lung	lung
39	chr2:233636200-233650000	Weak transcription	Fetal Brain Male	brain
40	chr2:233636200-233651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:233636200-233655200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:233636200-233655200	Weak transcription	NHLF	lung
43	chr2:233636200-233655400	Weak transcription	Esophagus	oesophagus
44	chr2:233636400-233643600	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:233636400-233649200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:233636400-233651800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:233636400-233651800	Weak transcription	NH-A	brain
48	chr2:233636400-233655000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:233636600-233643400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:233636800-233642000	Weak transcription	Primary hematopoietic stem cells	blood

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