Variant report

Variant	rs35322088
Chromosome Location	chr18:12653940-12653941
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	CEBPB	chr18:12653806-12653977	K562	blood:	n/a	n/a
2	CEBPB	chr18:12653806-12654027	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12648702..12654959-chr18:12655130..12658770,8	K562	blood:
2	chr18:12543497..12545408-chr18:12653876..12656459,2	MCF-7	breast:
3	chr18:12643422..12646156-chr18:12653146..12655533,3	MCF-7	breast:
4	chr18:12649857..12654959-chr18:12655130..12658770,11	K562	blood:

Variant related genes	Relation type
ENSG00000215527	TF binding region
SPIRE1	TF binding region
PSMG2	TF binding region
ENSG00000128789	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1062235	0.91[ASN][1000 genomes]
rs1129214	0.91[ASN][1000 genomes]
rs12373207	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12373259	0.89[ASN][1000 genomes]
rs12454322	0.83[EUR][1000 genomes]
rs12455268	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12455295	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12457771	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458097	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458895	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12954079	0.91[ASN][1000 genomes]
rs12957555	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12957603	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12957810	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12960623	0.95[ASN][1000 genomes]
rs12960997	0.91[ASN][1000 genomes]
rs12962598	0.91[ASN][1000 genomes]
rs12963505	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12964507	0.90[ASN][1000 genomes]
rs12965733	0.85[ASN][1000 genomes]
rs12965990	0.91[ASN][1000 genomes]
rs12966246	0.84[ASN][1000 genomes]
rs12966367	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12966424	0.91[ASN][1000 genomes]
rs12968771	0.95[ASN][1000 genomes]
rs12969300	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12969446	0.91[ASN][1000 genomes]
rs12969938	0.91[ASN][1000 genomes]
rs12971256	0.85[ASN][1000 genomes]
rs1362709	0.88[ASN][1000 genomes]
rs1549011	0.91[ASN][1000 genomes]
rs1592642	0.85[ASN][1000 genomes]
rs1592643	0.85[ASN][1000 genomes]
rs17616402	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971702	0.84[ASN][1000 genomes]
rs2011575	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011579	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051262	0.90[ASN][1000 genomes]
rs2302768	0.90[ASN][1000 genomes]
rs28820339	0.85[ASN][1000 genomes]
rs28832066	0.91[ASN][1000 genomes]
rs34040888	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34120824	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34277169	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34472716	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34537593	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34632667	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34690304	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34847769	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35506854	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35634465	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35699948	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35898717	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3809919	0.90[ASN][1000 genomes]
rs3902981	0.83[ASN][1000 genomes]
rs4296322	0.86[ASN][1000 genomes]
rs45589535	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45596833	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633785	0.91[ASN][1000 genomes]
rs55870255	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62095975	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096023	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096046	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62096048	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505760	0.85[ASN][1000 genomes]
rs66808227	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233175	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7233694	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7507018	0.91[ASN][1000 genomes]
rs8083182	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8083217	0.80[ASN][1000 genomes]
rs8086099	0.85[ASN][1000 genomes]
rs8086265	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8086846	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8097134	0.85[ASN][1000 genomes]
rs9303774	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303775	0.91[ASN][1000 genomes]
rs9303776	0.87[ASN][1000 genomes]
rs933600	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948319	0.90[ASN][1000 genomes]
rs963920	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945140	0.91[ASN][1000 genomes]
rs9945644	0.91[ASN][1000 genomes]
rs9945801	0.91[ASN][1000 genomes]
rs9948844	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9949293	0.91[ASN][1000 genomes]
rs9950365	0.91[ASN][1000 genomes]
rs9951576	0.91[ASN][1000 genomes]
rs9952000	0.91[ASN][1000 genomes]
rs9954112	0.91[ASN][1000 genomes]
rs9955985	0.91[ASN][1000 genomes]
rs9957880	0.90[ASN][1000 genomes]
rs9958100	0.88[ASN][1000 genomes]
rs9958412	0.91[ASN][1000 genomes]
rs9959039	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959458	0.91[ASN][1000 genomes]
rs9959536	0.90[ASN][1000 genomes]
rs9960555	0.90[ASN][1000 genomes]
rs9961799	0.85[ASN][1000 genomes]
rs9962006	0.91[ASN][1000 genomes]
rs9963809	0.85[ASN][1000 genomes]
rs9964868	0.92[ASN][1000 genomes]
rs9966464	0.88[ASN][1000 genomes]
rs9966490	0.90[ASN][1000 genomes]
rs9966672	0.90[ASN][1000 genomes]
rs9967437	0.91[ASN][1000 genomes]
rs9967553	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers 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 target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv576497	chr18:12650900-12658293	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv576498	chr18:12650900-12658436	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35322088	SPIRE1	cis	Muscle Skeletal	GTEx
rs35322088	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL
rs35322088	RP11-861E21.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
2	chr18:12646000-12654000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:12646400-12656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:12646400-12656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12646400-12657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:12648000-12656800	Weak transcription	Left Ventricle	heart
9	chr18:12648400-12656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12648600-12655800	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:12648600-12656800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:12650000-12654400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr18:12651000-12654000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:12651800-12654000	Enhancers	Brain Hippocampus Middle	brain
15	chr18:12652200-12655400	Enhancers	Fetal Brain Male	brain
16	chr18:12652400-12654000	Enhancers	Adipose Nuclei	Adipose
17	chr18:12652400-12654000	Enhancers	HUVEC	blood vessel
18	chr18:12652600-12654000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr18:12652600-12655400	Weak transcription	Fetal Kidney	kidney
20	chr18:12652800-12654200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:12653000-12654000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr18:12653000-12655800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr18:12653200-12656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:12653200-12656600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:12653200-12656600	Weak transcription	Right Atrium	heart
26	chr18:12653200-12656600	Weak transcription	Right Ventricle	heart
27	chr18:12653200-12656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:12653200-12656800	Weak transcription	Esophagus	oesophagus
29	chr18:12653200-12657000	Weak transcription	Spleen	Spleen
30	chr18:12653400-12654000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:12653400-12654000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr18:12653400-12654000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr18:12653400-12654200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:12653400-12655400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr18:12653400-12655400	Weak transcription	NHEK	skin
38	chr18:12653400-12655600	Weak transcription	HMEC	breast
39	chr18:12653400-12656400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr18:12653400-12656400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr18:12653400-12656600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr18:12653400-12656600	Weak transcription	Aorta	Aorta
43	chr18:12653400-12656600	Weak transcription	Psoas Muscle	Psoas
44	chr18:12653400-12657000	Weak transcription	Pancreas	Pancrea
45	chr18:12653400-12657000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr18:12653600-12655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr18:12653600-12655000	Active TSS	Fetal Brain Female	brain
48	chr18:12653600-12655200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr18:12653600-12655200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr18:12653600-12655400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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