Variant report

Variant	rs3817859
Chromosome Location	chr1:169819065-169819066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169763242..169766140-chr1:169817412..169820013,2	K562	blood:
2	chr1:169817987..169820044-chr1:169861944..169863561,2	K562	blood:
3	chr1:169818930..169821400-chr1:169825229..169828152,2	K562	blood:
4	chr1:169818623..169820125-chr1:169861453..169863170,2	MCF-7	breast:
5	chr1:169816746..169819328-chr1:169826032..169828001,2	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10489175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577641	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11578817	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11579102	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11579709	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581959	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11582552	0.86[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap]
rs11585093	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11589659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11589671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11590604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572551	1.00[CEU][hapmap]
rs16828209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16862683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16862705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16862902	1.00[CEU][hapmap]
rs1928887	1.00[CEU][hapmap]
rs2420510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34657513	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35196850	0.83[EUR][1000 genomes]
rs3753312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766150	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap]
rs4656198	0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs4656201	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656202	1.00[CEU][hapmap]
rs4656718	0.89[ASW][hapmap]
rs4656720	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656722	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656723	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656732	1.00[CEU][hapmap]
rs55806711	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57805301	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58111285	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60191157	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60315765	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61807812	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61807813	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61807814	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61807817	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61807818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61807835	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61807840	0.83[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026253	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers 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	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169823600	Weak transcription	Gastric	stomach
2	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
4	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
5	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
6	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:169786600-169841400	Strong transcription	Dnd41	blood
8	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
9	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
10	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:169802200-169822600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:169802400-169821800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:169802800-169819800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:169806400-169820600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
18	chr1:169808200-169819800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:169808200-169822000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:169808600-169821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:169808600-169827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:169808800-169823200	Weak transcription	Fetal Heart	heart
24	chr1:169809200-169829400	Strong transcription	GM12878-XiMat	blood
25	chr1:169809200-169829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:169810000-169828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:169810400-169841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:169810600-169841200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:169810800-169841000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:169810800-169841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:169811000-169841400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:169811400-169819600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:169811400-169825600	Strong transcription	HSMM	muscle
34	chr1:169811400-169827200	Strong transcription	K562	blood
35	chr1:169811600-169841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:169811800-169827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:169811800-169836200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:169811800-169841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:169812000-169840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:169812200-169820800	Weak transcription	Fetal Kidney	kidney
41	chr1:169812800-169836400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:169813000-169822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:169813200-169819200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:169813400-169841200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:169813600-169819600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:169814000-169819200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:169814200-169838000	Strong transcription	Placenta	Placenta
48	chr1:169814400-169819200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:169814400-169830400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum

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