Variant report

Variant	rs9333279
Chromosome Location	chr2:183793383-183793384
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	chr2:183790872-183793821	K562	blood:	n/a	n/a

Variant related genes	Relation type
NCKAP1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10177344	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187158	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10187800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1022337	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10497618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10931055	0.82[AFR][1000 genomes]
rs12470377	0.81[AMR][1000 genomes]
rs13385317	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13399354	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823924	0.89[CHB][hapmap]
rs2271671	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2368352	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28429165	0.88[EUR][1000 genomes]
rs28832369	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35285912	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3791247	0.88[CHB][hapmap]
rs4392211	0.81[AMR][1000 genomes]
rs4427983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666603	0.82[AFR][1000 genomes]
rs62190103	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62190104	0.82[AFR][1000 genomes]
rs6719673	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6730114	0.81[AMR][1000 genomes]
rs6735144	0.81[AMR][1000 genomes]
rs7510	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562515	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9333280	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183757400-183797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:183765600-183805200	Weak transcription	Gastric	stomach
3	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
5	chr2:183772400-183799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
8	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
9	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
10	chr2:183780000-183807000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:183780400-183800800	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
13	chr2:183780800-183811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:183781000-183798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:183781200-183798200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:183781200-183805800	Weak transcription	Fetal Heart	heart
17	chr2:183782200-183795400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:183782200-183814200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:183782400-183794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:183783000-183799600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:183784600-183804400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:183784800-183811400	Strong transcription	Fetal Intestine Large	intestine
23	chr2:183785800-183803800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:183785800-183824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:183786000-183794800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:183786000-183795000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:183786000-183803800	Strong transcription	HSMM	muscle
28	chr2:183786000-183804400	Strong transcription	HUVEC	blood vessel
29	chr2:183786200-183793400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:183786200-183798400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:183786200-183804200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:183786400-183800000	Weak transcription	Fetal Brain Female	brain
33	chr2:183786400-183814200	Weak transcription	Aorta	Aorta
34	chr2:183786600-183826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:183787000-183793800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:183787000-183824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:183787200-183793800	Strong transcription	HepG2	liver
38	chr2:183787600-183795200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr2:183788000-183830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:183788200-183845600	Weak transcription	Lung	lung
41	chr2:183788400-183794600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:183788400-183795800	Strong transcription	K562	blood
43	chr2:183788400-183798000	Weak transcription	Fetal Stomach	stomach
44	chr2:183788400-183798200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:183788400-183809600	Strong transcription	NH-A	brain
46	chr2:183788400-183811600	Weak transcription	Right Ventricle	heart
47	chr2:183788600-183798000	Weak transcription	Fetal Intestine Small	intestine
48	chr2:183789200-183806200	Weak transcription	Brain Angular Gyrus	brain
49	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:183789400-183811600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links