Variant report

Variant	rs7258807
Chromosome Location	chr19:36536938-36536939
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	chr19:36498459..36500910-chr19:36535292..36537978,3	MCF-7	breast:
2	chr19:36534753..36537195-chr19:36544858..36547286,2	K562	blood:

Variant related genes	Relation type
ENSG00000181392	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000075702	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1009381	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10406862	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418079	0.85[YRI][hapmap]
rs10419924	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420345	0.87[ASN][1000 genomes]
rs10421377	0.87[ASN][1000 genomes]
rs10422055	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs10425700	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10427033	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11538454	0.95[ASN][1000 genomes]
rs11666192	0.89[ASN][1000 genomes]
rs11669890	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12462159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12608517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981698	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs2023866	0.86[ASN][1000 genomes]
rs2074435	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141959	0.82[ASN][1000 genomes]
rs2227260	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2231568	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2301734	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2301737	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2871649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4555271	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4806249	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4806254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4806262	0.87[ASN][1000 genomes]
rs4806271	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806273	0.83[ASN][1000 genomes]
rs4806276	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55849299	0.98[ASN][1000 genomes]
rs6510516	0.89[YRI][hapmap]
rs7250364	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7251912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257026	0.85[ASN][1000 genomes]
rs73036134	0.87[ASN][1000 genomes]
rs8112640	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7258807	ZNF420	cis	cerebellum	SCAN
rs7258807	CYP2A7	cis	parietal	SCAN
rs7258807	ZNF527	cis	cerebellum	SCAN
rs7258807	PHLDB3	cis	cerebellum	SCAN
rs7258807	MEGF8	cis	cerebellum	SCAN
rs7258807	PHLDB3	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
3	chr19:36524000-36537000	Weak transcription	Small Intestine	intestine
4	chr19:36524200-36543800	Weak transcription	Left Ventricle	heart
5	chr19:36524200-36544000	Weak transcription	Primary B cells from cord blood	blood
6	chr19:36524200-36544400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:36524200-36544400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:36524200-36544400	Weak transcription	Aorta	Aorta
9	chr19:36524400-36537200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:36524400-36537200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:36524400-36543800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:36524400-36544000	Weak transcription	Fetal Lung	lung
13	chr19:36524600-36537000	Weak transcription	Brain Anterior Caudate	brain
14	chr19:36526400-36544200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:36526600-36540200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:36526600-36544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:36526800-36544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:36527000-36544600	Weak transcription	Gastric	stomach
19	chr19:36528400-36544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:36528600-36543800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:36528600-36543800	Weak transcription	Fetal Thymus	thymus
22	chr19:36528600-36544000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:36528600-36544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:36528600-36544400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:36528600-36544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:36530400-36537600	Weak transcription	Right Ventricle	heart
27	chr19:36530400-36544200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:36530400-36544400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:36530600-36537200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:36530600-36543800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr19:36530600-36544000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr19:36530600-36544400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:36530800-36537200	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:36530800-36537400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:36530800-36543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:36530800-36543800	Weak transcription	Brain Germinal Matrix	brain
37	chr19:36530800-36543800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:36531000-36543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:36531000-36543800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:36531000-36543800	Weak transcription	Fetal Muscle Leg	muscle
41	chr19:36531000-36544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:36531000-36544000	Weak transcription	Esophagus	oesophagus
43	chr19:36531200-36537400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:36531200-36543800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:36531200-36544000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr19:36531400-36544000	Weak transcription	Spleen	Spleen
47	chr19:36531800-36537400	Weak transcription	Fetal Intestine Small	intestine
48	chr19:36531800-36541400	Weak transcription	Fetal Stomach	stomach
49	chr19:36531800-36543600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:36532600-36543800	Weak transcription	Fetal Intestine Large	intestine

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