Variant report

Variant	rs10874980
Chromosome Location	chr1:92283899-92283900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92283210..92285190-chr1:92295185..92297126,2	K562	blood:

Variant related genes	Relation type
ENSG00000239794	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1032255	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs11165578	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11576557	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs11799400	1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs12027931	0.81[JPT][hapmap]
rs1352438	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1805109	0.83[CHD][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs1805110	0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs2046737	0.86[JPT][hapmap]
rs2087300	0.85[ASN][1000 genomes]
rs2129972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2129973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs2256471	0.90[ASN][1000 genomes]
rs2265863	0.85[ASN][1000 genomes]
rs2391070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs2450926	0.86[JPT][hapmap]
rs2489169	0.81[ASN][1000 genomes]
rs2489176	0.89[ASN][1000 genomes]
rs2489178	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2489184	0.84[ASN][1000 genomes]
rs2489185	0.84[ASN][1000 genomes]
rs2489186	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs2489189	0.85[MEX][hapmap]
rs2634019	0.86[JPT][hapmap]
rs2634023	0.86[JPT][hapmap]
rs2634024	0.86[JPT][hapmap]
rs2634025	0.85[JPT][hapmap]
rs2634028	0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs2634030	0.85[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs2634032	0.85[ASN][1000 genomes]
rs2634033	0.85[ASN][1000 genomes]
rs2634034	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2634036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs2799512	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs2799516	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2799517	0.85[ASN][1000 genomes]
rs2799522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2799523	0.88[JPT][hapmap]
rs2799524	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs2799526	0.85[JPT][hapmap]
rs2799539	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2799547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2810903	0.86[ASN][1000 genomes]
rs284146	0.89[ASN][1000 genomes]
rs284148	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs284150	0.89[ASN][1000 genomes]
rs284151	0.89[ASN][1000 genomes]
rs284156	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs284157	0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs284160	1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs284161	0.81[JPT][hapmap]
rs284162	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs284163	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs284164	1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs3103332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs3103333	0.87[ASN][1000 genomes]
rs428815	1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs449960	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs717923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs7550856	0.84[JPT][hapmap]
rs901913	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs901914	0.89[ASN][1000 genomes]
rs901915	0.89[ASN][1000 genomes]
rs901917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10874980	EPHX4	cis	cerebellum	SCAN
rs10874980	RPL5	cis	cerebellum	SCAN
rs10874980	GLMN	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92264800-92284200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92272400-92285400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:92275200-92284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:92275600-92292000	Weak transcription	Lung	lung
5	chr1:92276000-92284000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:92276400-92285000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:92277400-92291800	Enhancers	HepG2	liver
8	chr1:92277800-92286600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:92278000-92285200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:92278800-92288200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:92279600-92284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:92279600-92284600	Weak transcription	Left Ventricle	heart
13	chr1:92279600-92285000	Weak transcription	Esophagus	oesophagus
14	chr1:92279600-92285000	Weak transcription	Right Ventricle	heart
15	chr1:92279600-92287000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:92279600-92287200	Weak transcription	Spleen	Spleen
17	chr1:92279600-92294000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:92279800-92284200	Weak transcription	Right Atrium	heart
19	chr1:92280200-92285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:92280600-92286600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:92280800-92284400	Weak transcription	Hela-S3	cervix
22	chr1:92281000-92284800	Enhancers	Liver	Liver
23	chr1:92281000-92285600	Enhancers	Adipose Nuclei	Adipose
24	chr1:92281000-92285800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:92281000-92285800	Enhancers	Colon Smooth Muscle	Colon
26	chr1:92281000-92285800	Enhancers	Fetal Kidney	kidney
27	chr1:92281200-92286600	Enhancers	Fetal Heart	heart
28	chr1:92281200-92286600	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:92281400-92284000	Enhancers	NHDF-Ad	bronchial
30	chr1:92281400-92285600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:92281400-92285600	Enhancers	Fetal Lung	lung
32	chr1:92281600-92284000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:92281600-92284000	Weak transcription	HSMMtube	muscle
34	chr1:92281600-92285000	Weak transcription	Psoas Muscle	Psoas
35	chr1:92281600-92285000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:92281600-92285000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:92281600-92285000	Weak transcription	HUVEC	blood vessel
38	chr1:92281600-92285200	Weak transcription	Aorta	Aorta
39	chr1:92281600-92285200	Weak transcription	Small Intestine	intestine
40	chr1:92282000-92284200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:92282000-92285800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:92282000-92287400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:92282200-92287200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:92282400-92286000	Enhancers	Fetal Stomach	stomach
45	chr1:92282600-92284200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:92282600-92285400	Enhancers	Fetal Muscle Leg	muscle
47	chr1:92282800-92284400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr1:92282800-92285400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:92282800-92285400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:92283000-92284200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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