Variant report

Variant	rs4427983
Chromosome Location	chr2:183785598-183785599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183781828..183783867-chr2:183783906..183785691,2	MCF-7	breast:
2	chr2:183778975..183782738-chr2:183784220..183787705,4	K562	blood:
3	chr2:183783194..183785818-chr2:183787179..183789437,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJC10-5	chr2:183784638-183787512	NONHSAT075926

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10177344	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10187158	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10187800	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1022337	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10497618	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931052	0.81[ASW][hapmap];0.80[MEX][hapmap]
rs10931053	0.81[ASW][hapmap]
rs10931055	0.84[AFR][1000 genomes]
rs12470377	0.81[AMR][1000 genomes]
rs13385317	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13399354	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16823924	0.88[CHB][hapmap]
rs2271671	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2368352	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28429165	0.87[EUR][1000 genomes]
rs28832369	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791247	0.88[CHB][hapmap]
rs4392211	0.81[AMR][1000 genomes]
rs4666603	0.84[AFR][1000 genomes]
rs62190103	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62190104	0.84[AFR][1000 genomes]
rs6719673	0.81[EUR][1000 genomes]
rs6730114	0.81[AMR][1000 genomes]
rs6735144	0.81[AMR][1000 genomes]
rs7510	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562515	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7566668	0.81[ASW][hapmap];0.80[MEX][hapmap]
rs9288088	0.81[ASW][hapmap]
rs9333279	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9333280	0.81[ASW][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes]
rs9789450	0.81[ASW][hapmap];0.80[MEX][hapmap]

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	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	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
6	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4427983	FRZB	cis	cerebellum	SCAN
rs4427983	NCKAP1	cis	parietal	SCAN
rs4427983	ZNF804A	cis	cerebellum	SCAN
rs4427983	NCKAP1	cis	cerebellum	SCAN
rs4427983	DUSP19	cis	parietal	SCAN

Chromatin state (count:96 , 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	chr2:183765200-183792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:183765600-183805200	Weak transcription	Gastric	stomach
4	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
6	chr2:183770600-183786000	Weak transcription	Brain Substantia Nigra	brain
7	chr2:183770800-183787200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:183772400-183791000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:183772400-183799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:183772800-183786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
13	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
14	chr2:183773600-183793000	Weak transcription	Fetal Brain Male	brain
15	chr2:183775000-183787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
17	chr2:183776200-183786000	Weak transcription	Aorta	Aorta
18	chr2:183777800-183787200	Weak transcription	HepG2	liver
19	chr2:183778800-183786200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:183779000-183792800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:183780000-183792800	Weak transcription	Psoas Muscle	Psoas
22	chr2:183780000-183807000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:183780400-183785600	Weak transcription	Brain Anterior Caudate	brain
24	chr2:183780400-183787400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:183780400-183788400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:183780400-183788600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:183780400-183790400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:183780400-183792400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:183780400-183800800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
31	chr2:183780600-183791000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:183780600-183792800	Weak transcription	Ovary	ovary
33	chr2:183780800-183786000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:183780800-183811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:183781000-183787000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:183781000-183798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:183781200-183786000	Weak transcription	NH-A	brain
38	chr2:183781200-183786200	Weak transcription	Placenta	Placenta
39	chr2:183781200-183788600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:183781200-183789800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:183781200-183791000	Weak transcription	NHLF	lung
42	chr2:183781200-183798200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:183781200-183805800	Weak transcription	Fetal Heart	heart
44	chr2:183781400-183786200	Weak transcription	Adipose Nuclei	Adipose
45	chr2:183781400-183786200	Weak transcription	HSMMtube	muscle
46	chr2:183781400-183790800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:183781400-183792200	Weak transcription	Hela-S3	cervix
48	chr2:183781400-183793000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:183781800-183790400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:183782200-183795400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links