Variant report

Variant	rs4080606
Chromosome Location	chr19:42960486-42960487
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42947132..42948888-chr19:42958718..42960967,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189377	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10084159	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10401271	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10402677	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10403517	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405445	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405646	0.81[AMR][1000 genomes]
rs10405906	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407576	0.80[AMR][1000 genomes]
rs10412463	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10413413	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416089	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10419378	0.80[AMR][1000 genomes]
rs10420796	0.81[AMR][1000 genomes]
rs10422987	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10469271	0.81[AMR][1000 genomes]
rs10469284	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10469286	0.81[AMR][1000 genomes]
rs11665870	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665935	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666350	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666835	0.81[AMR][1000 genomes]
rs11666862	0.81[AMR][1000 genomes]
rs11668599	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11671272	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671846	0.93[EUR][1000 genomes]
rs11673645	0.93[EUR][1000 genomes]
rs11879306	0.96[EUR][1000 genomes]
rs11881517	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882150	0.96[EUR][1000 genomes]
rs12611218	0.98[ASN][1000 genomes]
rs13343936	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975789	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16975865	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28411988	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55850134	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60313903	0.93[EUR][1000 genomes]
rs6509016	0.81[AFR][1000 genomes]
rs7253056	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102439	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8103285	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8103891	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106570	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8107152	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8107254	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107790	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112156	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851298	0.93[EUR][1000 genomes]
rs851301	0.96[EUR][1000 genomes]
rs851302	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42952400-42964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:42954400-42961000	Enhancers	Primary B cells from cord blood	blood
3	chr19:42954600-42961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:42955400-42964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:42955400-42964600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:42955800-42966400	Weak transcription	GM12878-XiMat	blood
7	chr19:42957000-42961400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:42957000-42961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:42957000-42966000	Weak transcription	Left Ventricle	heart
10	chr19:42957400-42964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:42957400-42970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:42959000-42960600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:42959000-42960600	Enhancers	Duodenum Mucosa	Duodenum
14	chr19:42959000-42961600	Enhancers	Fetal Intestine Small	intestine
15	chr19:42959200-42960600	Enhancers	HMEC	breast
16	chr19:42959200-42961000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr19:42959400-42960800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr19:42960000-42961400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:42960000-42964600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:42960000-42970200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:42960200-42960800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr19:42960200-42963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:42960200-42963400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:42960200-42964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:42960200-42970000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:42960400-42961400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:42960400-42961400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:42960400-42961400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:42960400-42961800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr19:42960400-42963200	Weak transcription	Adipose Nuclei	Adipose
32	chr19:42960400-42963200	Weak transcription	HepG2	liver
33	chr19:42960400-42965600	Weak transcription	Right Atrium	heart
34	chr19:42960400-42965800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr19:42960400-42965800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:42960400-42966000	Weak transcription	Esophagus	oesophagus
37	chr19:42960400-42971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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