Variant report

Variant	rs10407506
Chromosome Location	chr19:42549934-42549935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42549668..42552954-chr19:42572953..42575417,3	K562	blood:
2	chr19:42547674..42551178-chr19:42553478..42557347,4	K562	blood:

Variant related genes	Relation type
ENSG00000105737	Chromatin interaction
ENSG00000105732	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10500285	0.86[CHD][hapmap]
rs1056995	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs11878620	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs11878917	0.86[ASN][1000 genomes]
rs11880124	0.86[CHD][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs11883412	0.86[CHD][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs1205817	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs16975663	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17270169	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs17342067	1.00[JPT][hapmap]
rs17342284	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2303652	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs3736109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3745233	0.80[LWK][hapmap]
rs3826705	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs443239	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs454150	0.84[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap]
rs4803520	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs61195828	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs899661	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[MKK][hapmap];0.93[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	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	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	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
5	esv10559	chr19:42547869-42553974	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv579627	chr19:42549934-42553502	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	nsv579628	chr19:42549934-42553804	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42528400-42553000	Weak transcription	Spleen	Spleen
2	chr19:42535600-42555200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:42537000-42553200	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:42537000-42557200	Weak transcription	Fetal Kidney	kidney
5	chr19:42537200-42558600	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:42539000-42556400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42539400-42570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42539400-42572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:42540400-42572600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:42540600-42550800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42540600-42551000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:42540600-42551600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:42540800-42551000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr19:42540800-42551800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:42541800-42551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:42542600-42553400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:42542800-42556400	Weak transcription	Right Ventricle	heart
18	chr19:42543400-42556400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:42543800-42550200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:42544200-42552200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:42544200-42553600	Weak transcription	Pancreas	Pancrea
22	chr19:42544600-42550400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:42544800-42553400	Weak transcription	Gastric	stomach
24	chr19:42545200-42550800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:42546000-42556000	Weak transcription	Fetal Muscle Leg	muscle
26	chr19:42546600-42550200	Weak transcription	Brain Anterior Caudate	brain
27	chr19:42546600-42556800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:42546600-42557600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:42546600-42559000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:42547000-42556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:42547200-42555800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:42547800-42550400	Strong transcription	Fetal Stomach	stomach
33	chr19:42548600-42550400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:42548600-42551000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:42548800-42551600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:42549000-42550000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:42549200-42550200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr19:42549200-42550400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:42549200-42550400	Strong transcription	Aorta	Aorta
40	chr19:42549200-42550600	Strong transcription	Brain Germinal Matrix	brain
41	chr19:42549200-42551000	Strong transcription	Brain Angular Gyrus	brain
42	chr19:42549200-42551200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:42549600-42554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:42549600-42556400	Weak transcription	Fetal Brain Male	brain
45	chr19:42549800-42553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:42549800-42556400	Strong transcription	Fetal Brain Female	brain
47	chr19:42549800-42563200	Weak transcription	Fetal Intestine Small	intestine

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