Variant report

Variant	rs4389291
Chromosome Location	chr2:183774869-183774870
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:183773913..183775803-chr2:183777634..183779722,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NCKAP1-2	chr2:183774745-183774992	NONHSAT075924

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10187684	0.81[ASN][1000 genomes]
rs10204853	0.81[ASN][1000 genomes]
rs1022337	1.00[JPT][hapmap]
rs10497617	0.81[ASN][1000 genomes]
rs10931052	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[ASN][1000 genomes]
rs10931053	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[ASN][1000 genomes]
rs10931055	0.81[ASN][1000 genomes]
rs11899644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12470377	0.90[ASN][1000 genomes]
rs12611998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12612383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12617567	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12992669	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12994001	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs13009031	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13409111	0.81[ASN][1000 genomes]
rs1400130	0.90[ASN][1000 genomes]
rs16823896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16823906	0.90[ASN][1000 genomes]
rs16823936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2138486	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2368351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2675048	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2675049	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2675051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2675076	0.81[ASN][1000 genomes]
rs2705741	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2705748	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34192739	0.81[ASN][1000 genomes]
rs34254952	0.81[ASN][1000 genomes]
rs34644467	0.81[ASN][1000 genomes]
rs34873881	0.81[ASN][1000 genomes]
rs34930236	0.81[ASN][1000 genomes]
rs35368327	0.81[ASN][1000 genomes]
rs35720425	0.81[ASN][1000 genomes]
rs35971883	0.81[ASN][1000 genomes]
rs3791246	1.00[JPT][hapmap]
rs4255929	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341895	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4392211	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4414644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4666873	0.81[ASN][1000 genomes]
rs4666876	1.00[JPT][hapmap]
rs55739115	0.81[ASN][1000 genomes]
rs60326110	0.81[ASN][1000 genomes]
rs60543070	0.81[ASN][1000 genomes]
rs62190104	0.81[ASN][1000 genomes]
rs6434000	0.81[ASN][1000 genomes]
rs6434001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66829551	0.81[ASN][1000 genomes]
rs6714190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6718462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs6726085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs6730114	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6730183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6732015	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6735144	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6735651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6745341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs67966058	0.90[ASN][1000 genomes]
rs73042165	0.90[ASN][1000 genomes]
rs73980539	0.81[ASN][1000 genomes]
rs7566668	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[ASN][1000 genomes]
rs7589630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7597884	0.81[ASN][1000 genomes]
rs7605639	0.81[ASN][1000 genomes]
rs9288088	0.94[ASW][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs9333280	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[ASN][1000 genomes]
rs9789450	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1006265	chr2:183666013-183777604	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv536071	chr2:183666013-183777604	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4389291	NCKAP1	cis	parietal	SCAN

Chromatin state (count:94 , 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	chr2:183759200-183775000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:183759200-183775200	Weak transcription	Pancreas	Pancrea
4	chr2:183759600-183777000	Weak transcription	HSMMtube	muscle
5	chr2:183762000-183778000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:183762400-183775000	Weak transcription	Osteobl	bone
7	chr2:183762400-183775200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:183762600-183775800	Weak transcription	NHDF-Ad	bronchial
9	chr2:183762600-183778000	Weak transcription	NHLF	lung
10	chr2:183765200-183792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:183765600-183805200	Weak transcription	Gastric	stomach
12	chr2:183766800-183779400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:183767000-183776800	Weak transcription	Spleen	Spleen
14	chr2:183768200-183775200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:183768600-183775200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:183768600-183777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:183768600-183778200	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:183768600-183779800	Weak transcription	Fetal Heart	heart
19	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:183768800-183775800	Weak transcription	Liver	Liver
21	chr2:183769800-183778400	Weak transcription	HMEC	breast
22	chr2:183769800-183779400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
24	chr2:183770600-183786000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:183770800-183777800	Weak transcription	Fetal Lung	lung
26	chr2:183770800-183779400	Weak transcription	Fetal Brain Female	brain
27	chr2:183770800-183779600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:183770800-183787200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:183771200-183775000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:183772200-183775200	Weak transcription	Aorta	Aorta
31	chr2:183772400-183775000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:183772400-183775800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:183772400-183779600	Strong transcription	HSMM	muscle
34	chr2:183772400-183780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:183772400-183791000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:183772400-183799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:183772600-183775800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:183772600-183778800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:183772600-183778800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:183772800-183775200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:183772800-183777200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:183772800-183777600	Weak transcription	HUVEC	blood vessel
44	chr2:183772800-183779600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:183772800-183780000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:183772800-183786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:183773200-183775000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:183773200-183779600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:183773400-183779400	Weak transcription	Fetal Intestine Small	intestine
50	chr2:183773400-183779800	Weak transcription	Brain Hippocampus Middle	brain

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