Variant report

Variant	rs7246525
Chromosome Location	chr19:41737996-41737997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41730351..41733971-chr19:41737087..41743441,7	K562	blood:
2	chr19:41730730..41737018-chr19:41737152..41743219,7	K562	blood:
3	chr19:41734780..41738564-chr19:41748060..41751187,3	K562	blood:
4	chr19:41736676..41739290-chr19:41770146..41772060,2	MCF-7	breast:
5	chr19:41731580..41733703-chr19:41737172..41738750,2	MCF-7	breast:
6	chr19:41737149..41740146-chr19:41745201..41747116,2	MCF-7	breast:
7	chr19:41735933..41738836-chr19:41743059..41745644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105323	Chromatin interaction
ENSG00000167601	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10421990	0.90[CHB][hapmap]
rs11879562	0.90[CHB][hapmap]
rs11882467	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs12327659	0.90[CHB][hapmap]
rs12462203	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12975585	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12978098	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978323	0.85[CHB][hapmap]
rs12979764	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980248	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980480	0.90[CHB][hapmap]
rs12983047	0.85[CHB][hapmap]
rs12984621	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1865051	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1865053	0.90[CHB][hapmap]
rs2304230	0.90[CHB][hapmap]
rs2304234	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3745295	0.90[CHB][hapmap]
rs3752705	0.90[CHB][hapmap]
rs3816052	0.90[CHB][hapmap]
rs3826714	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4456618	0.90[CHB][hapmap]
rs4802111	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802112	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4802113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803448	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803449	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs6508974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67033402	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6957	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7245398	0.90[CHB][hapmap]
rs7248164	0.90[CHB][hapmap]
rs7257310	0.85[CHB][hapmap]
rs7258749	0.90[CHB][hapmap]
rs8109167	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8109627	0.85[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3353863	chr19:41734412-41738010	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7246525	ERF	cis	cerebellum	SCAN
rs7246525	FOSB	cis	parietal	SCAN
rs7246525	ZNF226	cis	cerebellum	SCAN
rs7246525	BAX	cis	cerebellum	SCAN
rs7246525	ZNF155	cis	parietal	SCAN
rs7246525	FLT3LG	cis	cerebellum	SCAN
rs7246525	SIX5	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
3	chr19:41732800-41739200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:41732800-41742800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:41732800-41745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:41733000-41738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:41733000-41739200	Weak transcription	Placenta	Placenta
8	chr19:41733000-41739400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:41733000-41739400	Weak transcription	Ovary	ovary
10	chr19:41733000-41740200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:41733000-41743000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:41733000-41743200	Weak transcription	Right Ventricle	heart
13	chr19:41733000-41743600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:41733000-41743600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:41733000-41743600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:41733000-41743600	Weak transcription	Esophagus	oesophagus
17	chr19:41733000-41743600	Weak transcription	Spleen	Spleen
18	chr19:41733000-41743800	Weak transcription	Colonic Mucosa	Colon
19	chr19:41733000-41744200	Weak transcription	Gastric	stomach
20	chr19:41733000-41745200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:41733200-41738000	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:41733200-41738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:41733200-41739400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:41733200-41739400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:41733200-41739600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:41733200-41740600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr19:41733200-41741400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:41733200-41745400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:41733200-41746000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:41733200-41749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:41733200-41767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:41733200-41767200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr19:41733600-41739000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:41733800-41739400	Weak transcription	Fetal Intestine Small	intestine
35	chr19:41733800-41744800	Weak transcription	Fetal Intestine Large	intestine
36	chr19:41734000-41748600	Weak transcription	Hela-S3	cervix
37	chr19:41734200-41739400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:41734200-41740200	Weak transcription	HSMMtube	muscle
39	chr19:41734600-41739800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:41734800-41738000	Weak transcription	HUVEC	blood vessel
41	chr19:41735400-41741600	Strong transcription	NHEK	skin
42	chr19:41735600-41738200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:41736000-41739000	Strong transcription	NHDF-Ad	bronchial
44	chr19:41736000-41752400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:41736000-41767200	Strong transcription	Osteobl	bone
46	chr19:41736000-41767400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:41736200-41743800	Weak transcription	Brain Anterior Caudate	brain
48	chr19:41736200-41745200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:41736200-41757000	Strong transcription	NH-A	brain
50	chr19:41736400-41741800	Strong transcription	HMEC	breast

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