Variant report

Variant	rs2783495
Chromosome Location	chr1:93643677-93643678
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	chr1:93643610-93644056	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr1:93643550-93643912	K562	blood:	n/a	n/a
3	EP300	chr1:93643604-93643923	K562	blood:	n/a	n/a
4	WRNIP1	chr1:93643635-93643871	GM12878	blood:	n/a	n/a
5	MXI1	chr1:93643106-93647204	SK-N-SH	brain:	n/a	n/a
6	FOS	chr1:93643536-93643894	HUVEC	blood vessel:	n/a	chr1:93643725-93643736
7	FOSL2	chr1:93643541-93643987	SK-N-SH	brain:	n/a	n/a
8	FOS	chr1:93643574-93643888	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
9	FOS	chr1:93643573-93643921	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
10	ARID3A	chr1:93643373-93643843	K562	blood:	n/a	chr1:93643543-93643559
11	FOS	chr1:93643561-93643921	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
12	MYC	chr1:93643589-93644371	MCF10A-Er-Src	breast:	n/a	n/a
13	CHD1	chr1:93643454-93647252	IMR90	lung:	n/a	chr1:93645456-93645466

No.	Distal block	Cell Line	Cell type
1	chr1:93643262..93645748-chr1:94311384..94313517,2	K562	blood:
2	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
3	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
4	chr1:93542817..93546420-chr1:93641583..93645468,3	MCF-7	breast:

Variant related genes	Relation type
CCDC18	TF binding region
ENSG00000251795	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1010476	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1060622	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10782959	0.97[CHD][hapmap];0.83[GIH][hapmap]
rs10874766	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164870	0.82[CHB][hapmap]
rs11164876	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs11164879	0.81[CHB][hapmap]
rs11164896	0.86[EUR][1000 genomes]
rs11164905	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11164908	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12027142	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12030549	0.82[CHB][hapmap]
rs12030843	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12033147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12038046	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12038699	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs12044557	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs12044883	0.89[CHB][hapmap]
rs12045001	0.86[EUR][1000 genomes]
rs12046063	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12118262	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs12128131	0.89[CHB][hapmap]
rs12133576	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12563120	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs12563709	0.86[EUR][1000 genomes]
rs1335679	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1474927	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs1559828	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1572343	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1856027	0.85[CHD][hapmap]
rs2031225	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2255722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281524	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2281525	0.90[CHB][hapmap]
rs2295423	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2296558	0.81[CHB][hapmap]
rs2391254	0.82[CHB][hapmap]
rs2484486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749732	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2765545	0.92[CHD][hapmap]
rs2783489	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs2783490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783493	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783496	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783499	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2783500	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2783501	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2783504	0.83[ASN][1000 genomes]
rs2783505	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2815406	0.94[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815415	0.85[ASN][1000 genomes]
rs2815429	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28782525	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2893242	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754186	0.82[CHB][hapmap]
rs3767964	0.82[CHB][hapmap]
rs3904665	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3904666	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4000699	0.82[CHB][hapmap]
rs4240966	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4484937	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4847235	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4847240	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4847399	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4847408	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs489183	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs531358	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs556446	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs579138	0.80[ASN][1000 genomes]
rs612037	0.82[CHB][hapmap]
rs61799470	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61799496	0.83[ASN][1000 genomes]
rs61799497	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61799517	0.86[EUR][1000 genomes]
rs622608	0.81[CHB][hapmap]
rs6541349	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs6541401	0.82[CHB][hapmap]
rs6541404	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs6682670	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs6703310	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs693737	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs7513705	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7517363	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs7525248	0.85[CHB][hapmap]
rs7535628	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7539307	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs797668	0.82[CHB][hapmap]
rs797680	0.82[CHB][hapmap]
rs942196	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2783495	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs2783495	CCDC18	cis	parietal	SCAN
rs2783495	LRRC8D	cis	parietal	SCAN
rs2783495	GLMN	cis	cerebellum	SCAN
rs2783495	CCDC18	cis	multi-tissue	Pritchard
rs2783495	DR1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
4	chr1:93636200-93644000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:93636200-93644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:93636400-93643800	Weak transcription	Fetal Stomach	stomach
7	chr1:93638200-93644000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:93640200-93643800	Weak transcription	Aorta	Aorta
9	chr1:93641000-93644000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:93641600-93644000	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr1:93641600-93645000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:93641800-93643800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:93642000-93644000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:93642000-93644200	Enhancers	Small Intestine	intestine
15	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:93642200-93644400	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
18	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:93642400-93643800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:93642400-93645200	Weak transcription	Spleen	Spleen
21	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:93642600-93644600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:93642600-93647800	Active TSS	K562	blood
24	chr1:93642800-93644000	Enhancers	Fetal Muscle Leg	muscle
25	chr1:93642800-93644400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
27	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:93643000-93643800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:93643000-93643800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:93643000-93644600	Weak transcription	Esophagus	oesophagus
31	chr1:93643000-93644600	Weak transcription	Lung	lung
32	chr1:93643000-93644600	Flanking Active TSS	HUVEC	blood vessel
33	chr1:93643000-93645600	Active TSS	Right Atrium	heart
34	chr1:93643000-93646000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:93643000-93647600	Active TSS	NHLF	lung
37	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
38	chr1:93643200-93643800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
39	chr1:93643200-93643800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:93643200-93643800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:93643200-93644000	Genic enhancers	Primary T cells from cord blood	blood
42	chr1:93643200-93644200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:93643200-93644200	Flanking Active TSS	Osteobl	bone
44	chr1:93643200-93644600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:93643200-93644800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:93643200-93646000	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
48	chr1:93643200-93647400	Active TSS	A549	lung
49	chr1:93643200-93647600	Active TSS	HMEC	breast
50	chr1:93643400-93643800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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