Variant report

Variant	rs2004903
Chromosome Location	chr1:150941944-150941945
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	POLR2A	chr1:150941922-150942033	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:150941769-150942114	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000231073	TF binding region
CERS2	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10399947	0.83[AMR][1000 genomes]
rs10888397	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10888398	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204739	0.88[ASN][1000 genomes]
rs11204742	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11204743	0.92[ASN][1000 genomes]
rs11204747	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204748	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204749	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204750	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11579736	0.84[ASN][1000 genomes]
rs11581757	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11583707	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11589886	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12059949	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067685	0.87[ASN][1000 genomes]
rs12075597	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12090215	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12097963	0.88[ASN][1000 genomes]
rs12405726	0.86[ASN][1000 genomes]
rs12410869	0.85[AMR][1000 genomes]
rs12562939	0.87[ASN][1000 genomes]
rs1546376	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1889741	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972060	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2124952	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271076	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272214	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280627	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864882	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867296	0.86[ASN][1000 genomes]
rs2867297	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34985895	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36008098	0.85[AMR][1000 genomes]
rs3843843	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3849279	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4451553	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4970928	0.89[ASN][1000 genomes]
rs4970929	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4970930	0.93[ASN][1000 genomes]
rs4970931	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970980	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4970982	0.88[ASN][1000 genomes]
rs4970984	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970985	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970986	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4970987	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970988	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59024312	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587542	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658066	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6677420	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66847267	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6686064	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72704679	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72704682	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72704685	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7518156	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752376	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528773	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7556451	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556661	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8444	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs897815	0.89[ASN][1000 genomes]
rs9661876	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	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/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2004903	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2004903	RP11-98D18.3	cis	Esophagus Mucosa	GTEx
rs2004903	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2004903	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2004903	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs2004903	RP11-316M1.12	cis	Artery Aorta	GTEx
rs2004903	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs2004903	RP11-316M1.12	cis	Artery Tibial	GTEx
rs2004903	GOLPH3L	cis	Nerve Tibial	GTEx
rs2004903	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs2004903	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs2004903	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs2004903	RP11-316M1.12	cis	lung	GTEx
rs2004903	CTSS	cis	Thyroid	GTEx
rs2004903	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs2004903	HORMAD1	cis	Nerve Tibial	GTEx
rs2004903	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2004903	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2004903	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2004903	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs2004903	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2004903	RP11-316M1.12	cis	Whole Blood	GTEx
rs2004903	RP11-316M1.12	cis	Thyroid	GTEx
rs2004903	CTSS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150899600-150943400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:150900400-150942600	Weak transcription	Stomach Mucosa	stomach
3	chr1:150900400-150944200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:150903600-150942200	Strong transcription	Dnd41	blood
5	chr1:150903600-150942800	Strong transcription	Fetal Stomach	stomach
6	chr1:150903600-150943000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:150903600-150943200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:150903800-150942600	Strong transcription	Fetal Thymus	thymus
9	chr1:150904600-150942200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:150904600-150942400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:150904600-150942400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:150904600-150943400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:150905000-150942000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:150905000-150942400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:150905000-150943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:150905400-150942800	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:150905600-150942000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:150906200-150942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:150907000-150942200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:150907000-150942400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:150927000-150942400	Strong transcription	Primary B cells from cord blood	blood
22	chr1:150929400-150942200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:150929400-150942400	Strong transcription	Brain Germinal Matrix	brain
24	chr1:150929600-150942000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:150931400-150943000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:150931600-150942200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:150931600-150942200	Strong transcription	NHLF	lung
28	chr1:150932000-150943000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:150932000-150943400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:150932800-150942200	Strong transcription	NHEK	skin
31	chr1:150934600-150942800	Strong transcription	K562	blood
32	chr1:150935200-150942000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:150937000-150942200	Strong transcription	Spleen	Spleen
34	chr1:150937400-150942200	Strong transcription	Placenta	Placenta
35	chr1:150938200-150943200	Genic enhancers	Brain Anterior Caudate	brain
36	chr1:150940200-150942800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:150940200-150943000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:150940200-150944600	Weak transcription	Fetal Brain Male	brain
39	chr1:150940400-150943200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:150940400-150945200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:150940600-150942400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:150940800-150942400	Genic enhancers	Fetal Intestine Large	intestine
43	chr1:150940800-150942600	Genic enhancers	HepG2	liver
44	chr1:150940800-150945200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:150941000-150942200	Weak transcription	Right Atrium	heart
46	chr1:150941000-150943400	Genic enhancers	Fetal Intestine Small	intestine
47	chr1:150941000-150943400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:150941000-150943400	Weak transcription	NH-A	brain
49	chr1:150941000-150943600	Enhancers	Brain Angular Gyrus	brain
50	chr1:150941000-150944000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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