Variant report

Variant	rs56179717
Chromosome Location	chr2:183816575-183816576
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	chr2:183816494-183817682	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:183816568..183818121-chr2:183820543..183822285,2	K562	blood:
2	chr2:183799066..183801918-chr2:183816085..183818420,2	K562	blood:

Variant related genes	Relation type
NCKAP1	TF binding region
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11885629	1.00[EUR][1000 genomes]
rs11885833	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11888086	1.00[EUR][1000 genomes]
rs11892717	1.00[EUR][1000 genomes]
rs11896088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823829	1.00[EUR][1000 genomes]
rs16823945	1.00[EUR][1000 genomes]
rs16823948	1.00[EUR][1000 genomes]
rs16823949	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823966	1.00[EUR][1000 genomes]
rs4358084	1.00[EUR][1000 genomes]
rs55803212	1.00[EUR][1000 genomes]
rs55886059	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56344408	1.00[EUR][1000 genomes]
rs56362542	1.00[EUR][1000 genomes]
rs57047150	1.00[EUR][1000 genomes]
rs58515193	1.00[EUR][1000 genomes]
rs59308931	1.00[EUR][1000 genomes]
rs60558126	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60602756	1.00[EUR][1000 genomes]
rs6733333	1.00[EUR][1000 genomes]
rs6736252	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6742298	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6757286	1.00[EUR][1000 genomes]
rs73037284	1.00[EUR][1000 genomes]
rs73040079	1.00[EUR][1000 genomes]
rs73040083	1.00[EUR][1000 genomes]
rs73040085	1.00[EUR][1000 genomes]
rs73040088	1.00[EUR][1000 genomes]
rs73042107	1.00[EUR][1000 genomes]
rs73042129	1.00[EUR][1000 genomes]
rs73042136	1.00[EUR][1000 genomes]
rs73042149	1.00[EUR][1000 genomes]
rs73042166	1.00[EUR][1000 genomes]
rs73046211	1.00[EUR][1000 genomes]
rs73046213	1.00[EUR][1000 genomes]
rs73046217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046218	1.00[EUR][1000 genomes]
rs73046222	1.00[EUR][1000 genomes]
rs73046226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046235	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046257	1.00[EUR][1000 genomes]
rs73046260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73048203	1.00[EUR][1000 genomes]
rs73980523	1.00[EUR][1000 genomes]
rs73980527	1.00[EUR][1000 genomes]
rs7558834	1.00[EUR][1000 genomes]
rs7561870	1.00[EUR][1000 genomes]
rs7584932	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7601416	1.00[EUR][1000 genomes]
rs7602182	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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
5	esv3693446	chr2:183785598-183833514	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
2	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
3	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
4	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
5	chr2:183785800-183824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:183786600-183826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:183787000-183824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:183788000-183830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:183788200-183845600	Weak transcription	Lung	lung
10	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:183790800-183824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:183793400-183840800	Weak transcription	Fetal Brain Male	brain
13	chr2:183793600-183823800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:183793600-183826600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:183795200-183824200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:183798600-183847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:183800200-183817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:183802800-183817800	Weak transcription	Fetal Brain Female	brain
20	chr2:183803800-183826600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:183803800-183826600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:183804800-183859600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:183807400-183824200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:183812000-183816600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:183812000-183817400	Weak transcription	Fetal Kidney	kidney
27	chr2:183812000-183819600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:183812000-183821200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:183812000-183839000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:183812000-183857800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:183812200-183816600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:183812200-183816800	Weak transcription	NHLF	lung
33	chr2:183812200-183819600	Weak transcription	Right Atrium	heart
34	chr2:183812200-183820400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:183812200-183826200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:183812200-183826200	Weak transcription	Left Ventricle	heart
37	chr2:183812200-183826600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:183812200-183832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:183812200-183833000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:183812200-183838200	Weak transcription	Small Intestine	intestine
41	chr2:183812200-183842000	Weak transcription	Right Ventricle	heart
42	chr2:183812200-183874800	Weak transcription	Gastric	stomach
43	chr2:183812400-183831200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:183812400-183856800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:183813200-183819600	Strong transcription	HepG2	liver
46	chr2:183813400-183823200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:183813600-183819000	Strong transcription	Fetal Intestine Large	intestine
48	chr2:183813600-183823800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:183813800-183818400	Strong transcription	Liver	Liver
50	chr2:183814000-183817000	Strong transcription	Fetal Muscle Leg	muscle

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