Variant report

Variant	rs10409428
Chromosome Location	chr19:42831816-42831817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42758717..42760946-chr19:42831370..42833314,2	MCF-7	breast:
2	chr19:42589152..42591857-chr19:42830713..42833464,2	K562	blood:
3	chr19:42788208..42790691-chr19:42829217..42832174,3	K562	blood:

Variant related genes	Relation type
ENSG00000105722	Chromatin interaction
ENSG00000268643	Chromatin interaction
ENSG00000079432	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10401224	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10402438	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404650	1.00[EUR][1000 genomes]
rs10406800	0.86[YRI][hapmap]
rs10406972	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407085	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407155	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407842	1.00[EUR][1000 genomes]
rs10408258	1.00[EUR][1000 genomes]
rs10409433	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10410653	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10411498	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs10411908	1.00[EUR][1000 genomes]
rs10413484	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10414056	0.85[YRI][hapmap]
rs10415478	0.85[YRI][hapmap]
rs10415999	1.00[EUR][1000 genomes]
rs10416241	0.85[YRI][hapmap]
rs10416535	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs10418312	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs10421409	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10421510	0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421857	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs10422301	1.00[EUR][1000 genomes]
rs10422867	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423812	0.91[AFR][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	0.85[AFR][1000 genomes]
rs10425003	1.00[EUR][1000 genomes]
rs10425320	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10425783	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426267	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426284	1.00[EUR][1000 genomes]
rs11878207	0.93[YRI][hapmap];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[YRI][hapmap];1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[YRI][hapmap];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	0.93[YRI][hapmap];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]
rs28572784	0.85[YRI][hapmap]
rs28657829	1.00[EUR][1000 genomes]
rs28663042	1.00[EUR][1000 genomes]
rs28675019	1.00[EUR][1000 genomes]
rs28675764	1.00[EUR][1000 genomes]
rs28699037	1.00[EUR][1000 genomes]
rs28711448	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715574	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[YRI][hapmap];1.00[EUR][1000 genomes]
rs73552879	1.00[EUR][1000 genomes]
rs73554520	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73554531	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8099885	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs8109258	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9304602	0.89[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
7	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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830200-42832000	Flanking Active TSS	Dnd41	blood
2	chr19:42830600-42832000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:42830600-42840200	Weak transcription	Aorta	Aorta
4	chr19:42830800-42832000	Enhancers	Brain Hippocampus Middle	brain
5	chr19:42830800-42832000	Enhancers	Brain Substantia Nigra	brain
6	chr19:42830800-42832000	Enhancers	Gastric	stomach
7	chr19:42830800-42832200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:42830800-42832400	Weak transcription	Placenta	Placenta
9	chr19:42830800-42832400	Enhancers	Spleen	Spleen
10	chr19:42830800-42832600	Enhancers	Adipose Nuclei	Adipose
11	chr19:42830800-42832600	Enhancers	Fetal Muscle Trunk	muscle
12	chr19:42830800-42832800	Enhancers	Lung	lung
13	chr19:42830800-42833400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:42830800-42833400	Enhancers	Ovary	ovary
15	chr19:42830800-42833600	Enhancers	Pancreas	Pancrea
16	chr19:42830800-42840000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:42830800-42840200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:42830800-42840400	Weak transcription	Colonic Mucosa	Colon
19	chr19:42830800-42840400	Weak transcription	A549	lung
20	chr19:42830800-42840600	Weak transcription	Primary B cells from cord blood	blood
21	chr19:42830800-42841000	Weak transcription	HSMMtube	muscle
22	chr19:42830800-42851200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:42830800-42856400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:42830800-42867200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:42830800-42867600	Weak transcription	Fetal Kidney	kidney
26	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
27	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr19:42831000-42832000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr19:42831000-42832600	Enhancers	Left Ventricle	heart
30	chr19:42831000-42832600	Enhancers	Rectal Smooth Muscle	rectum
31	chr19:42831000-42832800	Enhancers	Psoas Muscle	Psoas
32	chr19:42831000-42833400	Enhancers	Fetal Intestine Large	intestine
33	chr19:42831000-42839400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:42831000-42840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:42831000-42840400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:42831000-42840400	Weak transcription	Osteobl	bone
37	chr19:42831000-42843600	Weak transcription	Right Atrium	heart
38	chr19:42831000-42856200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:42831000-42860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:42831000-42874400	Weak transcription	HSMM	muscle
41	chr19:42831200-42832000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:42831200-42832400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:42831200-42832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:42831200-42832600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:42831200-42832600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:42831200-42832600	Enhancers	Brain Anterior Caudate	brain
47	chr19:42831200-42832800	Enhancers	Fetal Intestine Small	intestine
48	chr19:42831200-42833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:42831200-42833200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr19:42831200-42833800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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