Variant report

Variant	rs2368352
Chromosome Location	chr2:183832438-183832439
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	POLR2A	chr2:183831876-183833778	K562	blood:	n/a	n/a
2	JUND	chr2:183832185-183832445	HepG2	liver:	n/a	chr2:183832340-183832349 chr2:183832315-183832324 chr2:183832314-183832325 chr2:183832316-183832324 chr2:183832317-183832324 chr2:183832316-183832325

No.	Distal block	Cell Line	Cell type
1	chr2:183826876..183828751-chr2:183831035..183834010,2	K562	blood:
2	chr2:183817340..183818993-chr2:183832231..183833794,2	MCF-7	breast:
3	chr2:183816933..183819427-chr2:183831655..183834604,2	K562	blood:

Variant related genes	Relation type
NCKAP1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10177344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187158	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187800	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10221950	0.84[ASN][1000 genomes]
rs1022337	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10497618	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931055	0.85[AFR][1000 genomes]
rs13385317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823924	0.89[CHB][hapmap]
rs2271671	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429165	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28832369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35285912	0.86[ASN][1000 genomes]
rs3791247	0.88[CHB][hapmap]
rs4427983	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666603	0.85[AFR][1000 genomes]
rs62190103	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62190104	0.85[AFR][1000 genomes]
rs6719673	0.88[ASN][1000 genomes]
rs7510	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562515	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9333279	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]

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	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
5	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
6	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 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	chr2:183788200-183845600	Weak transcription	Lung	lung
6	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:183793400-183840800	Weak transcription	Fetal Brain Male	brain
8	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:183798600-183847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:183804800-183859600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:183812000-183839000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:183812000-183857800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:183812200-183832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:183812200-183833000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:183812200-183838200	Weak transcription	Small Intestine	intestine
17	chr2:183812200-183842000	Weak transcription	Right Ventricle	heart
18	chr2:183812200-183874800	Weak transcription	Gastric	stomach
19	chr2:183812400-183856800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:183814600-183874800	Weak transcription	Aorta	Aorta
21	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:183814800-183845600	Weak transcription	Ovary	ovary
23	chr2:183815000-183833200	Weak transcription	Fetal Heart	heart
24	chr2:183815800-183832800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:183816000-183832800	Weak transcription	Psoas Muscle	Psoas
26	chr2:183818600-183860400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:183820000-183833000	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:183820000-183838600	Weak transcription	Brain Anterior Caudate	brain
29	chr2:183820000-183850800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:183820400-183833200	Weak transcription	Brain Substantia Nigra	brain
31	chr2:183821600-183841200	Weak transcription	Hela-S3	cervix
32	chr2:183821800-183833000	Weak transcription	Fetal Brain Female	brain
33	chr2:183822400-183841800	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:183822600-183837200	Weak transcription	Fetal Kidney	kidney
35	chr2:183824200-183832600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:183824200-183839400	Weak transcription	HSMMtube	muscle
37	chr2:183825400-183834800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:183825600-183834000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:183825600-183834000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:183825600-183835400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:183826200-183833800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:183826200-183833800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:183826400-183834000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:183826400-183834200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:183826400-183834600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:183826600-183833200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:183826600-183833600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:183826600-183833800	Strong transcription	HSMM	muscle
49	chr2:183826600-183833800	Strong transcription	HUVEC	blood vessel
50	chr2:183826600-183833800	Strong transcription	NHDF-Ad	bronchial

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