Variant report

Variant	rs10425320
Chromosome Location	chr19:42871692-42871693
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	chr19:42865401..42867644-chr19:42869322..42871775,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10401224	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10402438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404650	1.00[EUR][1000 genomes]
rs10406972	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407085	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407842	1.00[EUR][1000 genomes]
rs10408258	1.00[EUR][1000 genomes]
rs10409428	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409433	1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	1.00[EUR][1000 genomes]
rs10410653	1.00[EUR][1000 genomes]
rs10411498	1.00[EUR][1000 genomes]
rs10411908	1.00[EUR][1000 genomes]
rs10413484	1.00[EUR][1000 genomes]
rs10415999	1.00[EUR][1000 genomes]
rs10416535	1.00[EUR][1000 genomes]
rs10418312	1.00[EUR][1000 genomes]
rs10421409	1.00[EUR][1000 genomes]
rs10421510	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10421857	1.00[EUR][1000 genomes]
rs10422301	1.00[EUR][1000 genomes]
rs10422867	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423812	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423959	1.00[EUR][1000 genomes]
rs10423978	1.00[EUR][1000 genomes]
rs10424402	1.00[EUR][1000 genomes]
rs10424939	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425003	1.00[EUR][1000 genomes]
rs10425783	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426284	1.00[EUR][1000 genomes]
rs11878207	1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11880356	1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[EUR][1000 genomes]
rs13343388	1.00[EUR][1000 genomes]
rs13343719	1.00[EUR][1000 genomes]
rs13343761	1.00[EUR][1000 genomes]
rs13343834	1.00[EUR][1000 genomes]
rs13343966	1.00[EUR][1000 genomes]
rs13346837	1.00[EUR][1000 genomes]
rs2229614	1.00[EUR][1000 genomes]
rs28463673	1.00[EUR][1000 genomes]
rs28469564	1.00[EUR][1000 genomes]
rs28474957	1.00[EUR][1000 genomes]
rs28483598	1.00[EUR][1000 genomes]
rs28496975	1.00[EUR][1000 genomes]
rs28657829	1.00[EUR][1000 genomes]
rs28663042	1.00[EUR][1000 genomes]
rs28675019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675764	1.00[EUR][1000 genomes]
rs28699037	1.00[EUR][1000 genomes]
rs28711448	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28715574	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33919763	1.00[EUR][1000 genomes]
rs35707383	1.00[EUR][1000 genomes]
rs36089262	1.00[EUR][1000 genomes]
rs59870753	1.00[EUR][1000 genomes]
rs60950516	1.00[EUR][1000 genomes]
rs7246232	1.00[EUR][1000 genomes]
rs7248473	1.00[EUR][1000 genomes]
rs7254853	1.00[EUR][1000 genomes]
rs7255343	1.00[EUR][1000 genomes]
rs7258727	1.00[EUR][1000 genomes]
rs73552879	1.00[EUR][1000 genomes]
rs73554520	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73554531	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8099885	1.00[EUR][1000 genomes]
rs8109258	1.00[EUR][1000 genomes]
rs9304602	1.00[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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
2	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr19:42831000-42874400	Weak transcription	HSMM	muscle
4	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:42831800-42873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:42831800-42874800	Weak transcription	K562	blood
7	chr19:42844800-42877400	Weak transcription	Stomach Mucosa	stomach
8	chr19:42857800-42874000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:42858200-42872200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:42862400-42873800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:42862600-42878800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:42863600-42874800	Weak transcription	HUVEC	blood vessel
13	chr19:42865200-42873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:42868400-42873800	Weak transcription	Placenta	Placenta
15	chr19:42868400-42874000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:42868400-42874400	Strong transcription	Fetal Intestine Small	intestine
17	chr19:42868400-42874800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:42868400-42874800	Weak transcription	NHLF	lung
19	chr19:42868400-42874800	Weak transcription	Osteobl	bone
20	chr19:42868400-42876200	Weak transcription	Lung	lung
21	chr19:42868400-42879200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:42868400-42881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:42868400-42882400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:42868600-42873600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:42868600-42873800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:42868600-42873800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:42868600-42874000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:42868600-42878800	Weak transcription	Esophagus	oesophagus
29	chr19:42868600-42878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr19:42868600-42879000	Weak transcription	Aorta	Aorta
31	chr19:42868600-42882600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:42868800-42871800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:42868800-42872400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:42868800-42872400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:42868800-42873400	Weak transcription	Fetal Lung	lung
36	chr19:42868800-42874800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:42868800-42874800	Weak transcription	NH-A	brain
38	chr19:42868800-42874800	Weak transcription	NHEK	skin
39	chr19:42868800-42878800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr19:42868800-42878800	Weak transcription	Gastric	stomach
41	chr19:42868800-42878800	Weak transcription	Thymus	Thymus
42	chr19:42868800-42878800	Weak transcription	Dnd41	blood
43	chr19:42868800-42880800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:42868800-42882000	Strong transcription	Fetal Stomach	stomach
45	chr19:42869000-42872200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:42869000-42872200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:42869000-42872200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:42869000-42872400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:42869000-42872600	Enhancers	Fetal Heart	heart
50	chr19:42869000-42873000	Weak transcription	Spleen	Spleen

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