Variant report

Variant	rs6707924
Chromosome Location	chr2:98433908-98433909
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98426137..98428822-chr2:98433655..98435579,2	K562	blood:
2	chr2:98427986..98429941-chr2:98431797..98434605,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10176201	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10182941	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10200949	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10211231	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1071885	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865055	0.82[AFR][1000 genomes]
rs11123924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123949	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123966	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11690482	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11693874	0.82[AFR][1000 genomes]
rs11888323	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11899171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712123	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712174	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13003978	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13006817	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13008503	0.81[ASN][1000 genomes]
rs13010946	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13022778	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13034644	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1317178	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13405546	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1466924	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1503200	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1922280	0.89[ASN][1000 genomes]
rs1922282	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2017028	0.82[AFR][1000 genomes]
rs2091772	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2100058	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141862	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2309316	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309317	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309356	0.82[ASN][1000 genomes]
rs3762593	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4274643	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4560167	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5865	0.91[ASN][1000 genomes]
rs6543108	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6543109	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543161	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543177	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543202	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543210	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709571	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6710813	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723466	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6723653	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744331	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748809	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6748927	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7558931	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7561104	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7562695	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7567397	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574437	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7577886	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7582664	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598116	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7602412	0.82[AFR][1000 genomes]
rs7605180	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs930607	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9308862	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs956696	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9973416	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking 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	28 gene(s)	inside rSNPs	diseases
2	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6707924	ZAP70	cis	Nerve Tibial	GTEx
rs6707924	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98387800-98438200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
4	chr2:98406400-98469200	Weak transcription	A549	lung
5	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
6	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
7	chr2:98410000-98435800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98410000-98446000	Weak transcription	Colonic Mucosa	Colon
9	chr2:98410000-98456200	Weak transcription	Thymus	Thymus
10	chr2:98410000-98456800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:98410000-98456800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:98410000-98457400	Weak transcription	Small Intestine	intestine
13	chr2:98422000-98436200	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:98422000-98456200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:98423800-98437200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:98424000-98438600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:98424000-98442600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:98424000-98446800	Weak transcription	Fetal Heart	heart
19	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:98424800-98436600	Strong transcription	Primary B cells from cord blood	blood
22	chr2:98425600-98456800	Weak transcription	Esophagus	oesophagus
23	chr2:98425600-98461000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:98426000-98445400	Weak transcription	Gastric	stomach
25	chr2:98426000-98456800	Weak transcription	Right Ventricle	heart
26	chr2:98426200-98435600	Weak transcription	Aorta	Aorta
27	chr2:98426200-98456800	Weak transcription	Pancreas	Pancrea
28	chr2:98426400-98436600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:98426400-98437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:98426400-98456200	Weak transcription	NHEK	skin
31	chr2:98426400-98456800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:98427000-98436000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:98427600-98435200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:98428000-98466600	Weak transcription	K562	blood
35	chr2:98428200-98456600	Weak transcription	Brain Angular Gyrus	brain
36	chr2:98428400-98447400	Weak transcription	Psoas Muscle	Psoas
37	chr2:98428600-98436400	Weak transcription	Spleen	Spleen
38	chr2:98428600-98447400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:98428600-98448800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:98428600-98456000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:98428600-98456600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:98428600-98461200	Weak transcription	Fetal Brain Male	brain
43	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
44	chr2:98428800-98437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:98428800-98485000	Weak transcription	NHLF	lung
46	chr2:98429000-98438600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:98429200-98438400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:98429200-98448600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:98429200-98448800	Weak transcription	Fetal Kidney	kidney

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