Variant report

Variant	rs1962049
Chromosome Location	chr7:66240522-66240523
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66233619..66236445-chr7:66238794..66241787,2	MCF-7	breast:
2	chr7:66203830..66206564-chr7:66239736..66241863,2	K562	blood:
3	chr7:66232638..66234742-chr7:66239785..66241846,2	K562	blood:

Variant related genes	Relation type
ENSG00000154710	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000272831	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1622330	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1638736	0.87[CEU][hapmap]
rs34644698	1.00[AFR][1000 genomes]
rs66510832	0.86[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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1962049	VKORC1L1	cis	Whole Blood	GTEx
rs1962049	GUSB	cis	Whole Blood	GTEx
rs1962049	ASL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
3	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
4	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:66227000-66243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
7	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:66233000-66241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:66234200-66241800	Weak transcription	Small Intestine	intestine
11	chr7:66234800-66243600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:66235400-66241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
16	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
17	chr7:66236600-66241000	Strong transcription	Fetal Intestine Small	intestine
18	chr7:66236600-66244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:66236800-66242400	Strong transcription	HSMM	muscle
20	chr7:66236800-66242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:66236800-66243400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:66236800-66243800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:66236800-66244800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:66236800-66245400	Strong transcription	GM12878-XiMat	blood
25	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr7:66236800-66276800	Strong transcription	Dnd41	blood
28	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:66237000-66243800	Strong transcription	Fetal Thymus	thymus
31	chr7:66237000-66244800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:66237000-66245000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:66237000-66245400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:66237200-66244000	Strong transcription	Placenta	Placenta
35	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
36	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:66237400-66242000	Strong transcription	Fetal Stomach	stomach
38	chr7:66238000-66242200	Strong transcription	Spleen	Spleen
39	chr7:66238000-66243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:66238000-66246600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr7:66238000-66253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:66238200-66241000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:66238200-66241800	Strong transcription	Fetal Intestine Large	intestine
44	chr7:66238200-66242200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:66238200-66242200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:66238200-66242200	Strong transcription	Esophagus	oesophagus
47	chr7:66238200-66244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr7:66238200-66246600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:66238200-66247600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:66238200-66248800	Strong transcription	Primary B cells from cord blood	blood

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