Variant report

Variant	rs1807985
Chromosome Location	chr2:99957303-99957304
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	ZNF384	chr2:99957160-99957398	K562	blood:	n/a	n/a
2	FOSL2	chr2:99957288-99957692	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99770887..99773276-chr2:99955255..99957900,2	MCF-7	breast:

Variant related genes	Relation type
TXNDC9	TF binding region
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000273155	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1000409	0.87[EUR][1000 genomes]
rs10170425	0.85[EUR][1000 genomes]
rs10172068	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10172752	0.87[EUR][1000 genomes]
rs10186340	0.80[EUR][1000 genomes]
rs10187843	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779902	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123782	0.81[ASN][1000 genomes]
rs11123786	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11674219	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11679115	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683651	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11686535	0.81[ASN][1000 genomes]
rs11687870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11884686	0.88[ASN][1000 genomes]
rs11887109	0.88[EUR][1000 genomes]
rs11887574	0.84[EUR][1000 genomes]
rs11892441	0.82[ASN][1000 genomes]
rs11902994	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052986	0.85[ASN][1000 genomes]
rs12464535	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618779	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12621141	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12623540	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13008948	0.81[ASN][1000 genomes]
rs13017871	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13018274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13026997	0.81[ASN][1000 genomes]
rs13028869	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13389623	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13392042	0.87[EUR][1000 genomes]
rs13394688	0.81[EUR][1000 genomes]
rs13427780	0.85[EUR][1000 genomes]
rs1376443	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451243	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1584647	0.81[ASN][1000 genomes]
rs1584648	0.81[ASN][1000 genomes]
rs17022629	0.81[ASN][1000 genomes]
rs1901283	0.85[EUR][1000 genomes]
rs2141908	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2242037	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2290255	0.85[ASN][1000 genomes]
rs2290256	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305354	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2309576	0.88[ASN][1000 genomes]
rs2309585	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2309617	0.88[ASN][1000 genomes]
rs28369943	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs28382954	0.84[EUR][1000 genomes]
rs3087386	0.87[EUR][1000 genomes]
rs3791212	0.87[ASN][1000 genomes]
rs3792134	0.86[EUR][1000 genomes]
rs3792146	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3792149	0.87[EUR][1000 genomes]
rs3792152	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811555	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3828316	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4535093	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4850901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4850903	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851200	0.91[AMR][1000 genomes]
rs4851204	0.88[ASN][1000 genomes]
rs4851205	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55867742	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58086269	0.81[ASN][1000 genomes]
rs59178618	0.88[ASN][1000 genomes]
rs60294863	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61103312	0.82[ASN][1000 genomes]
rs62153855	0.81[ASN][1000 genomes]
rs6542879	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6542880	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6542882	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6708861	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709240	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713608	0.88[ASN][1000 genomes]
rs6713792	0.85[EUR][1000 genomes]
rs6714244	0.85[EUR][1000 genomes]
rs6717515	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6720885	0.86[ASN][1000 genomes]
rs6734290	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71413827	0.91[AFR][1000 genomes]
rs7558062	0.88[ASN][1000 genomes]
rs7558074	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561079	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567674	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7571202	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7574135	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7579403	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7580448	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7584127	0.82[ASN][1000 genomes]
rs7585721	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586892	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587419	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7589365	0.85[ASN][1000 genomes]
rs7591212	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593274	0.81[ASN][1000 genomes]
rs7597045	0.88[ASN][1000 genomes]
rs7598629	0.87[EUR][1000 genomes]
rs7601470	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601730	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7602923	0.88[ASN][1000 genomes]
rs7606977	0.88[ASN][1000 genomes]
rs7609108	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs959929	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1807985	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs1807985	REV1	cis	Thyroid	GTEx
rs1807985	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs1807985	LYG1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99951600-99958200	Active TSS	GM12878-XiMat	blood
2	chr2:99954800-99959000	Weak transcription	Lung	lung
3	chr2:99955000-99957400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:99955000-99958400	Enhancers	Liver	Liver
5	chr2:99955000-99959800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:99955000-99964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:99955000-99965400	Weak transcription	Gastric	stomach
8	chr2:99955000-99977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:99955000-99979200	Weak transcription	Fetal Stomach	stomach
10	chr2:99955000-99979800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:99955200-99961600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:99955200-99974400	Weak transcription	Thymus	Thymus
13	chr2:99955200-99979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
15	chr2:99955400-99957600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:99955400-99959000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:99955400-99964400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:99955400-99970000	Weak transcription	NHDF-Ad	bronchial
19	chr2:99955400-99976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:99955400-99979600	Weak transcription	NH-A	brain
22	chr2:99955600-99964600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:99955600-99978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:99955800-99961600	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:99955800-99976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:99956000-99957600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:99956000-99958000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:99956000-99963800	Weak transcription	Primary T cells from cord blood	blood
29	chr2:99956000-99976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:99956200-99957400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:99956200-99957800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:99956200-99957800	Enhancers	Hela-S3	cervix
33	chr2:99956200-99958000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:99956200-99964600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:99956200-99970200	Weak transcription	Osteobl	bone
36	chr2:99956200-99976600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:99956200-99977600	Weak transcription	Fetal Thymus	thymus
38	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
39	chr2:99956400-99958200	Enhancers	A549	lung
40	chr2:99956400-99958200	Enhancers	NHEK	skin
41	chr2:99956400-99962000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:99956400-99962200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:99956400-99964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
46	chr2:99956600-99959800	Enhancers	HepG2	liver
47	chr2:99956600-99977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:99956800-99957400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:99956800-99957600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:99956800-99957600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links