Variant report

Variant	rs1206042
Chromosome Location	chr19:42850253-42850254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42846856..42849578-chr19:42849783..42852178,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10410185	0.89[EUR][1000 genomes]
rs10410198	0.84[EUR][1000 genomes]
rs10410698	0.84[EUR][1000 genomes]
rs10412833	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1206009	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1206027	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206028	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1206029	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206031	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1206033	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1206035	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206038	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1206040	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206041	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206043	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209280	0.89[EUR][1000 genomes]
rs1211265	0.89[EUR][1000 genomes]
rs13346991	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1613100	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654623	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676211	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676213	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676214	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676215	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676217	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1676220	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1676221	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1676222	0.93[ASN][1000 genomes]
rs1685565	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2537697	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2615614	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28537976	0.84[EUR][1000 genomes]
rs28621009	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34922891	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35557987	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61995685	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255956	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260287	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73552881	0.84[EUR][1000 genomes]
rs73552895	0.93[EUR][1000 genomes]
rs851292	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851293	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851294	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs851296	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs851615	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs862228	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs865436	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9636121	0.80[AMR][1000 genomes];0.84[EUR][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42851200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr19:42830800-42856400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:42830800-42867200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:42830800-42867600	Weak transcription	Fetal Kidney	kidney
5	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
6	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:42831000-42856200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:42831000-42860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr19:42831000-42874400	Weak transcription	HSMM	muscle
10	chr19:42831200-42856600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:42831200-42856800	Weak transcription	Fetal Thymus	thymus
12	chr19:42831400-42867400	Weak transcription	Fetal Heart	heart
13	chr19:42831400-42867400	Weak transcription	NHEK	skin
14	chr19:42831600-42856400	Weak transcription	HMEC	breast
15	chr19:42831600-42856600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:42831600-42861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:42831800-42852200	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:42831800-42873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:42831800-42874800	Weak transcription	K562	blood
21	chr19:42833400-42867400	Weak transcription	GM12878-XiMat	blood
22	chr19:42835400-42867400	Strong transcription	Fetal Stomach	stomach
23	chr19:42836600-42861000	Weak transcription	Psoas Muscle	Psoas
24	chr19:42837400-42851600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:42839800-42866800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:42840200-42850800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr19:42841000-42858200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:42841000-42867600	Weak transcription	Osteobl	bone
29	chr19:42841200-42858400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:42841200-42859600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:42841400-42851800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:42841400-42855400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:42841400-42855800	Weak transcription	Brain Substantia Nigra	brain
34	chr19:42841400-42859800	Weak transcription	NHLF	lung
35	chr19:42841400-42861000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr19:42841400-42865000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:42841600-42851000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr19:42841600-42851200	Weak transcription	Primary B cells from cord blood	blood
39	chr19:42841600-42852000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr19:42841600-42855400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:42841600-42857400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:42841600-42860200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:42841600-42860400	Weak transcription	A549	lung
44	chr19:42841600-42867800	Weak transcription	HepG2	liver
45	chr19:42841800-42860600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:42843400-42867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:42844000-42861800	Strong transcription	Fetal Intestine Small	intestine
48	chr19:42844000-42867200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:42844200-42856000	Strong transcription	Brain Germinal Matrix	brain
50	chr19:42844400-42850400	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links