Variant report

Variant	rs4236559
Chromosome Location	chr7:101551566-101551567
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101545055..101547008-chr7:101551122..101553066,2	K562	blood:
2	chr7:101550263..101552814-chr7:101556063..101557676,3	K562	blood:
3	chr7:101544077..101549064-chr7:101550086..101553092,6	K562	blood:
4	chr7:101550842..101553432-chr7:101559510..101561361,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10229003	1.00[CHB][hapmap]
rs10245008	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs11768899	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs11971810	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729755	1.00[CHB][hapmap]
rs6465836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6957361	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6961254	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6978555	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6979596	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7780749	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4236559	PVRIG	cis	cerebellum	SCAN
rs4236559	PDAP1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
3	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
4	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
5	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:101535400-101554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:101535600-101554200	Weak transcription	HepG2	liver
8	chr7:101535600-101554600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:101535800-101555200	Weak transcription	Liver	Liver
10	chr7:101535800-101555600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:101537000-101554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:101537000-101554600	Weak transcription	Fetal Intestine Large	intestine
13	chr7:101537600-101559000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:101540000-101555600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:101540200-101559200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:101540400-101555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:101540400-101559200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:101541400-101554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:101541400-101555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:101541400-101555000	Weak transcription	Fetal Thymus	thymus
21	chr7:101542400-101555600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:101542600-101558000	Weak transcription	Dnd41	blood
23	chr7:101543600-101554400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:101544000-101555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:101544000-101558200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:101544000-101569800	Weak transcription	HMEC	breast
27	chr7:101544200-101554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:101544200-101559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:101544200-101559400	Weak transcription	NHEK	skin
30	chr7:101544200-101579800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:101544400-101555000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:101544400-101555200	Weak transcription	A549	lung
33	chr7:101544400-101556600	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:101544600-101556600	Weak transcription	Brain Germinal Matrix	brain
35	chr7:101545200-101553800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:101545600-101553000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr7:101545600-101554200	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:101545600-101554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:101545600-101554400	Weak transcription	Esophagus	oesophagus
40	chr7:101545600-101555600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr7:101545800-101553600	Weak transcription	Right Atrium	heart
42	chr7:101545800-101554200	Weak transcription	Fetal Lung	lung
43	chr7:101545800-101557000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:101546000-101554200	Weak transcription	Fetal Heart	heart
45	chr7:101546200-101554600	Weak transcription	Stomach Mucosa	stomach
46	chr7:101546600-101554200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:101546600-101556600	Weak transcription	Aorta	Aorta
48	chr7:101546800-101553400	Weak transcription	Placenta	Placenta
49	chr7:101546800-101553800	Weak transcription	Fetal Muscle Leg	muscle
50	chr7:101547000-101553000	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links