Variant report

Variant	rs2061299
Chromosome Location	chr8:103245444-103245445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103239162..103241164-chr8:103243127..103246074,2	K562	blood:
2	chr8:101962637..101964695-chr8:103242719..103245503,2	MCF-7	breast:
3	chr8:103232033..103234810-chr8:103243383..103246591,3	K562	blood:

Variant related genes	Relation type
ENSG00000164924	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10090707	0.82[MEX][hapmap]
rs10505020	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12707772	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs13248603	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13249865	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13250998	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13259151	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13261528	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13262662	0.84[EUR][1000 genomes]
rs13263132	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13269273	0.80[CEU][hapmap]
rs13269311	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13270908	0.87[EUR][1000 genomes]
rs13278798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs13278875	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28927991	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999669	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270914	0.81[EUR][1000 genomes]
rs34278087	0.81[EUR][1000 genomes]
rs34279135	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297513	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34351006	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34356268	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34730203	0.87[EUR][1000 genomes]
rs34976508	0.81[EUR][1000 genomes]
rs35166521	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35316247	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35558240	0.86[EUR][1000 genomes]
rs35558370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818724	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35873559	0.85[EUR][1000 genomes]
rs35969173	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35980679	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36178006	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4483125	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56003023	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572423	0.88[EUR][1000 genomes]
rs71518852	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650001	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650002	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2061299	ATP6V1C1	cis	cerebellum	SCAN
rs2061299	PIGY	trans	cerebellum	SCAN
rs2061299	KCNS2	cis	parietal	SCAN
rs2061299	RIMS2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
2	chr8:103216200-103247400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:103216400-103246600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr8:103217000-103248400	Weak transcription	Small Intestine	intestine
5	chr8:103217800-103246400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:103218000-103246200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:103219200-103247600	Weak transcription	Fetal Brain Male	brain
8	chr8:103220400-103248800	Weak transcription	Hela-S3	cervix
9	chr8:103222600-103246000	Strong transcription	Osteobl	bone
10	chr8:103227600-103246800	Strong transcription	Primary B cells from cord blood	blood
11	chr8:103229600-103246800	Strong transcription	Primary hematopoietic stem cells	blood
12	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr8:103236600-103245800	Strong transcription	HSMMtube	muscle
15	chr8:103237200-103248400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:103238200-103248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr8:103238400-103248200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr8:103238400-103248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:103239400-103246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:103240000-103246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:103240600-103246800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr8:103240800-103246600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:103240800-103247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr8:103240800-103247600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr8:103240800-103248800	Weak transcription	Pancreas	Pancrea
26	chr8:103240800-103249000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr8:103240800-103249000	Weak transcription	Gastric	stomach
28	chr8:103241000-103245800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:103241000-103246600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr8:103241000-103247200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:103241000-103248000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:103241000-103248200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr8:103241000-103248200	Weak transcription	Aorta	Aorta
34	chr8:103241000-103248400	Weak transcription	Lung	lung
35	chr8:103241000-103248400	Weak transcription	Thymus	Thymus
36	chr8:103241000-103248600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr8:103241000-103248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:103241000-103248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:103241000-103249000	Weak transcription	Right Ventricle	heart
40	chr8:103241000-103249200	Weak transcription	Colonic Mucosa	Colon
41	chr8:103241000-103250400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:103241000-103250400	Weak transcription	Esophagus	oesophagus
43	chr8:103241200-103248600	Weak transcription	Ovary	ovary
44	chr8:103241200-103249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:103241200-103249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr8:103241400-103248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:103241400-103249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr8:103241400-103250600	Weak transcription	Spleen	Spleen
49	chr8:103241600-103246600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:103242000-103249400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links