Variant report

Variant	rs4873619
Chromosome Location	chr8:48630687-48630688
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	chr8:48629245..48631641-chr8:48646004..48648559,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10957549	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10957644	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10958058	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1106607	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11778548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11784823	0.85[EUR][1000 genomes]
rs12544329	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12549996	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12675378	0.86[EUR][1000 genomes]
rs12678110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16928696	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1872840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2129617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2129618	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2130411	0.83[CEU][hapmap]
rs2130412	0.85[EUR][1000 genomes]
rs2130413	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4489323	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4608108	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4873368	0.84[EUR][1000 genomes]
rs4873395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4873399	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4873437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4873507	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4873529	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55941013	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56092229	0.89[EUR][1000 genomes]
rs62539116	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62539144	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62539147	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62539150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6982620	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6987043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6989917	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7014443	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7827571	0.82[CEU][hapmap]
rs876915	0.84[EUR][1000 genomes]
rs923499	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1026287	chr8:48615720-48710849	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv971233	chr8:48629417-48631557	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48597200-48647200	Weak transcription	NHEK	skin
2	chr8:48597200-48647400	Weak transcription	HMEC	breast
3	chr8:48602800-48647800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:48604400-48648400	Weak transcription	Small Intestine	intestine
5	chr8:48606800-48646400	Weak transcription	Fetal Heart	heart
6	chr8:48609200-48632400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:48611800-48632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:48612000-48647400	Weak transcription	NH-A	brain
9	chr8:48612400-48640000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:48613600-48632200	Weak transcription	Fetal Brain Female	brain
11	chr8:48613600-48636600	Weak transcription	NHDF-Ad	bronchial
12	chr8:48613600-48647200	Weak transcription	A549	lung
13	chr8:48615400-48632600	Weak transcription	Colon Smooth Muscle	Colon
14	chr8:48615800-48634200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:48616400-48632600	Weak transcription	Fetal Brain Male	brain
16	chr8:48618000-48638800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr8:48618000-48648800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr8:48618200-48651200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr8:48619200-48648400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:48619200-48649000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:48619600-48647600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:48623400-48631400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:48624200-48641600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr8:48624400-48647800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr8:48624600-48643800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr8:48624800-48635600	Weak transcription	K562	blood
27	chr8:48626200-48632200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:48626200-48638400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr8:48626200-48646000	Weak transcription	Colonic Mucosa	Colon
30	chr8:48626400-48632600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr8:48626400-48634800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr8:48626600-48632200	Weak transcription	Brain Germinal Matrix	brain
33	chr8:48626600-48632400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:48626600-48639200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr8:48626600-48646400	Weak transcription	Osteobl	bone
36	chr8:48626600-48646600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr8:48626600-48648200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr8:48626800-48631600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr8:48626800-48632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:48626800-48632200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr8:48626800-48632200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr8:48626800-48636800	Weak transcription	NHLF	lung
43	chr8:48626800-48638400	Weak transcription	Fetal Thymus	thymus
44	chr8:48626800-48644400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:48627000-48632200	Weak transcription	Aorta	Aorta
46	chr8:48627000-48632200	Weak transcription	HSMMtube	muscle
47	chr8:48627000-48632400	Weak transcription	Brain Substantia Nigra	brain
48	chr8:48627000-48632400	Weak transcription	Fetal Lung	lung
49	chr8:48627000-48632400	Weak transcription	HSMM	muscle
50	chr8:48627000-48632600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links