Variant report

Variant	rs2010506
Chromosome Location	chr19:19387356-19387357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:19387041-19387929	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19382597..19385606-chr19:19387254..19389947,3	K562	blood:
2	chr19:19386675..19389436-chr19:19391039..19392571,2	K562	blood:

Variant related genes	Relation type
TM6SF2	TF binding region
ENSG00000267629	TF binding region
ENSG00000105705	Chromatin interaction
ENSG00000267629	Chromatin interaction
ENSG00000213996	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10401714	0.94[EUR][1000 genomes]
rs10403273	0.96[EUR][1000 genomes]
rs10407933	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs10422893	0.95[EUR][1000 genomes]
rs10423874	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs1064395	0.93[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs11555053	0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1557723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1560687	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs17216041	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17751061	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1989867	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2011503	0.89[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060275	0.89[YRI][hapmap]
rs2074302	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2315023	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2916070	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs2965184	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2965186	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2965190	0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2965195	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2965201	0.88[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs35854118	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4239639	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808932	0.94[EUR][1000 genomes]
rs4808933	0.94[EUR][1000 genomes]
rs4808934	0.93[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4808944	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808951	0.89[YRI][hapmap]
rs4808962	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs55762233	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55765017	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55822665	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56044734	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56135441	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56144632	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56212061	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56278919	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57436187	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511027	0.93[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7257875	0.95[EUR][1000 genomes]
rs72999030	0.94[EUR][1000 genomes]
rs72999059	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72999063	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72999068	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs754256	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs756997	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs756999	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8100097	0.86[EUR][1000 genomes]
rs8100713	0.81[AFR][1000 genomes]
rs8105642	0.89[YRI][hapmap]
rs8108777	0.94[EUR][1000 genomes]
rs8110171	0.89[YRI][hapmap]
rs8110250	0.89[YRI][hapmap]
rs8113794	0.84[AFR][1000 genomes]
rs998732	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2010506	LSM4	cis	cerebellum	SCAN
rs2010506	OCEL1	cis	parietal	SCAN
rs2010506	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs2010506	IL12RB1	cis	parietal	SCAN
rs2010506	YJEFN3	cis	cerebellum	SCAN
rs2010506	DDX49	cis	cerebellum	SCAN
rs2010506	GATAD2A	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19381600-19387600	Weak transcription	K562	blood
2	chr19:19383800-19388400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:19384000-19388200	Weak transcription	HMEC	breast
4	chr19:19384200-19387400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:19384400-19388400	Weak transcription	Psoas Muscle	Psoas
6	chr19:19384400-19391600	Weak transcription	Hela-S3	cervix
7	chr19:19384400-19392200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:19384400-19430600	Weak transcription	Right Atrium	heart
9	chr19:19384600-19387600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:19384600-19388400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19384600-19389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:19384800-19387800	Enhancers	HSMMtube	muscle
13	chr19:19384800-19390400	Weak transcription	Fetal Brain Male	brain
14	chr19:19384800-19394000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:19384800-19403200	Weak transcription	HUVEC	blood vessel
16	chr19:19385000-19388200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:19385200-19388800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:19385200-19389600	Strong transcription	Fetal Brain Female	brain
19	chr19:19385200-19396400	Weak transcription	NHDF-Ad	bronchial
20	chr19:19385200-19403400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:19385400-19391000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:19385400-19393000	Strong transcription	Brain Germinal Matrix	brain
23	chr19:19385400-19409800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:19385400-19428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:19385600-19387400	ZNF genes & repeats	Lung	lung
26	chr19:19385600-19391000	Strong transcription	Brain Angular Gyrus	brain
27	chr19:19385600-19391200	Strong transcription	Brain Anterior Caudate	brain
28	chr19:19385600-19392800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:19385600-19392800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:19385600-19393400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:19385600-19395000	Strong transcription	Right Ventricle	heart
32	chr19:19385600-19396400	Strong transcription	Thymus	Thymus
33	chr19:19385600-19401200	Strong transcription	Primary T cells from cord blood	blood
34	chr19:19385600-19401600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:19385600-19403200	Strong transcription	Fetal Stomach	stomach
36	chr19:19385600-19403600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:19385600-19410000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:19385800-19388600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:19385800-19390600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:19385800-19391200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:19385800-19392200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:19385800-19392600	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr19:19385800-19395200	Strong transcription	Esophagus	oesophagus
44	chr19:19385800-19398200	Strong transcription	Left Ventricle	heart
45	chr19:19385800-19398600	Strong transcription	Brain Hippocampus Middle	brain
46	chr19:19385800-19399200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:19385800-19401200	Strong transcription	Adipose Nuclei	Adipose
48	chr19:19385800-19402200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:19385800-19402400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr19:19385800-19403200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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