Variant report

Variant	rs797681
Chromosome Location	chr1:93717746-93717747
allele	C/T
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	SPI1	chr1:93717570-93717849	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93716580..93719392-chr1:93724593..93726917,2	K562	blood:
2	chr1:93717455..93719072-chr1:93721833..93723353,2	K562	blood:

Variant related genes	Relation type
CCDC18	TF binding region

Extended variants
information (count: 136 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1000607	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1057257	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1060622	0.82[AMR][1000 genomes]
rs10782955	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10782957	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10874759	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10874762	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874764	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874772	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10874773	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874777	0.86[EUR][1000 genomes]
rs1088318	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164876	0.85[EUR][1000 genomes]
rs11164879	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164880	0.87[EUR][1000 genomes]
rs11164881	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164885	0.83[ASN][1000 genomes]
rs11164902	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164904	0.88[ASN][1000 genomes]
rs11576494	0.85[EUR][1000 genomes]
rs12030549	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030843	0.83[ASN][1000 genomes]
rs12031765	0.83[ASN][1000 genomes]
rs12038699	0.80[AMR][1000 genomes]
rs12044557	0.83[ASN][1000 genomes]
rs12044657	0.88[EUR][1000 genomes]
rs12044883	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12048219	0.82[ASN][1000 genomes]
rs12118230	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118262	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124011	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124771	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12130734	0.84[EUR][1000 genomes]
rs12133576	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12139009	0.82[AMR][1000 genomes]
rs12139633	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12406245	0.87[EUR][1000 genomes]
rs12752223	0.81[ASN][1000 genomes]
rs1335679	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1426318	0.87[EUR][1000 genomes]
rs1535699	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1535701	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1559828	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572343	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1593512	0.87[EUR][1000 genomes]
rs1932314	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2031225	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031226	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2152358	0.86[AMR][1000 genomes]
rs2295423	0.82[AMR][1000 genomes]
rs2295424	0.80[AMR][1000 genomes]
rs2296558	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297707	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391254	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2765545	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35940311	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3754186	0.97[ASN][1000 genomes]
rs3767962	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3767964	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904665	0.83[ASN][1000 genomes]
rs4000699	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4484937	0.83[ASN][1000 genomes]
rs4847235	0.85[EUR][1000 genomes]
rs4847240	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847402	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847406	0.91[ASN][1000 genomes]
rs4847408	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847410	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847412	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847419	0.87[EUR][1000 genomes]
rs4847420	0.87[EUR][1000 genomes]
rs531358	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs531514	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs535760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547866	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555161	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs565919	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs569414	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58354545	0.83[ASN][1000 genomes]
rs59417472	0.87[EUR][1000 genomes]
rs602204	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612037	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61799500	0.83[ASN][1000 genomes]
rs622608	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624131	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627779	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs637646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6541349	0.82[ASN][1000 genomes]
rs6541401	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541404	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6658257	0.82[ASN][1000 genomes]
rs6680022	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6680107	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6682670	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688230	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6694508	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6703310	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs682514	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687394	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72959220	0.83[ASN][1000 genomes]
rs7417952	0.87[EUR][1000 genomes]
rs7418101	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512911	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513705	0.89[EUR][1000 genomes]
rs7517363	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7524964	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7525248	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7526112	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532195	0.85[EUR][1000 genomes]
rs7535628	0.87[EUR][1000 genomes]
rs7537403	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539307	0.88[EUR][1000 genomes]
rs7540025	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541304	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541687	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547244	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551485	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553465	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553916	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs797661	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs797666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797668	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797671	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797672	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs797675	0.81[AMR][1000 genomes]
rs797676	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797680	0.83[AMR][1000 genomes]
rs942196	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432453	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432459	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432465	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9432681	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9660390	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs797681	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs797681	RP4-717I23.3	cis	Whole Blood	GTEx
rs797681	DR1	cis	Adipose Subcutaneous	GTEx
rs797681	RP4-717I23.3	cis	Artery Tibial	GTEx
rs797681	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs797681	DR1	cis	multi-tissue	Pritchard
rs797681	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs797681	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs797681	RP4-717I23.3	cis	Artery Aorta	GTEx
rs797681	CCDC18	cis	Nerve Tibial	GTEx
rs797681	RP4-717I23.3	cis	lung	GTEx
rs797681	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs797681	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs797681	RP4-717I23.3	cis	Thyroid	GTEx
rs797681	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs797681	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs797681	RP4-717I23.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
6	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
8	chr1:93706400-93727000	Weak transcription	K562	blood
9	chr1:93707000-93727400	Weak transcription	Liver	Liver
10	chr1:93708800-93720200	Weak transcription	NHLF	lung
11	chr1:93709000-93718200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:93709000-93718200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:93709000-93718400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:93709000-93718400	Weak transcription	Aorta	Aorta
15	chr1:93709000-93719000	Weak transcription	NHDF-Ad	bronchial
16	chr1:93709000-93719800	Weak transcription	HSMM	muscle
17	chr1:93709000-93720800	Weak transcription	Osteobl	bone
18	chr1:93709000-93724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:93709000-93726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:93709000-93727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:93709000-93728200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:93709000-93728200	Weak transcription	HMEC	breast
23	chr1:93709200-93718200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:93709200-93718400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:93709200-93718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:93709200-93718400	Weak transcription	Fetal Stomach	stomach
27	chr1:93709200-93727400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:93709400-93718400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:93709400-93718400	Weak transcription	Fetal Thymus	thymus
30	chr1:93709400-93718400	Weak transcription	A549	lung
31	chr1:93709400-93727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:93709600-93718200	Weak transcription	Primary T cells from cord blood	blood
33	chr1:93709600-93718400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:93709600-93719000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:93709600-93720200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:93709600-93725000	Weak transcription	HepG2	liver
37	chr1:93709600-93725600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:93709600-93727000	Weak transcription	NHEK	skin
39	chr1:93709800-93718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:93709800-93727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:93709800-93727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:93710000-93718200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:93710000-93718200	Weak transcription	Thymus	Thymus
44	chr1:93710000-93718400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:93710000-93721600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:93710000-93727000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:93710200-93721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:93710200-93722200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:93710200-93724200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:93710200-93727000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links