Variant report

Variant	rs7257846
Chromosome Location	chr19:18887677-18887678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18873859..18875560-chr19:18886840..18888488,3	K562	blood:
2	chr19:18836550..18839278-chr19:18885925..18888717,2	K562	blood:
3	chr19:18858094..18859912-chr19:18886098..18888648,2	K562	blood:
4	chr19:18875448..18876988-chr19:18887590..18889948,2	MCF-7	breast:
5	chr19:18885317..18890245-chr19:18892616..18897433,6	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12609934	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611313	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975249	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17757406	0.84[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1989888	0.88[ASN][1000 genomes]
rs2075017	0.85[TSI][hapmap]
rs2240014	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240887	0.84[GIH][hapmap]
rs28494505	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746266	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787050	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808852	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs56090467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510997	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs6510998	0.83[CEU][hapmap]
rs6510999	0.85[TSI][hapmap]
rs6511002	0.81[JPT][hapmap]
rs7256502	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs730079	0.81[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs739638	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][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	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv911295	chr19:18874483-18902592	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv911296	chr19:18874483-18915988	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3423006	chr19:18886977-18889825	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7257846	DDA1	cis	cerebellum	SCAN
rs7257846	COMP	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18854600-18895800	Weak transcription	Right Atrium	heart
2	chr19:18862600-18888400	Weak transcription	Aorta	Aorta
3	chr19:18865600-18894600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:18865600-18896000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:18868200-18890600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:18873800-18889200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:18873800-18889200	Weak transcription	Left Ventricle	heart
8	chr19:18873800-18895600	Weak transcription	Ovary	ovary
9	chr19:18873800-18896200	Weak transcription	Brain Angular Gyrus	brain
10	chr19:18875200-18889200	Weak transcription	Adipose Nuclei	Adipose
11	chr19:18876200-18888800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:18876400-18888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:18880200-18888000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr19:18880600-18888000	Strong transcription	Fetal Intestine Small	intestine
15	chr19:18880600-18888400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:18880600-18889400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:18880600-18895800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:18880800-18892600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr19:18882000-18890600	Weak transcription	Brain Anterior Caudate	brain
20	chr19:18882600-18888000	Weak transcription	Gastric	stomach
21	chr19:18883000-18889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:18883200-18888600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:18883400-18889200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:18883800-18888000	Weak transcription	Fetal Heart	heart
25	chr19:18884200-18893000	Weak transcription	Esophagus	oesophagus
26	chr19:18886000-18888400	Weak transcription	Right Ventricle	heart
27	chr19:18886000-18888600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:18886200-18888000	Enhancers	NHLF	lung
29	chr19:18886400-18888000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:18886400-18889600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:18886600-18887800	Enhancers	HSMM	muscle
32	chr19:18886600-18888000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:18886600-18888000	Enhancers	HMEC	breast
34	chr19:18886600-18888200	Enhancers	NHDF-Ad	bronchial
35	chr19:18886600-18888600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr19:18886800-18887800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:18886800-18887800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:18886800-18887800	Enhancers	A549	lung
39	chr19:18886800-18887800	Enhancers	HSMMtube	muscle
40	chr19:18886800-18888000	Bivalent Enhancer	Placenta	Placenta
41	chr19:18886800-18888000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:18886800-18888200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:18886800-18888400	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr19:18886800-18888800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:18887000-18888000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:18887000-18888000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:18887000-18888000	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:18887000-18888400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:18887200-18887800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr19:18887200-18887800	Weak transcription	Fetal Intestine Large	intestine

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