Variant report

Variant	rs11579102
Chromosome Location	chr1:169848330-169848331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169846979..169849303-chr1:169851464..169854908,3	K562	blood:
2	chr1:169846941..169849701-chr1:169857998..169859525,2	MCF-7	breast:
3	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
4	chr1:169846456..169849390-chr1:169863296..169865489,2	MCF-7	breast:
5	chr1:169846082..169850359-chr1:169859892..169864668,5	K562	blood:
6	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10489175	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10800488	0.85[EUR][1000 genomes]
rs11577641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11578817	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11579709	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11581959	0.93[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11582552	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap]
rs11585093	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11589659	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11589671	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11590604	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1360294	0.88[CEU][hapmap]
rs1572551	1.00[CEU][hapmap];0.96[AFR][1000 genomes]
rs16828209	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16862683	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16862705	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16862902	1.00[CEU][hapmap]
rs1928887	1.00[CEU][hapmap]
rs2420510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2420511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34657513	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35196850	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3753312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766139	0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766146	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766150	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3817859	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]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap]
rs4656198	0.89[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs4656201	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656202	1.00[CEU][hapmap]
rs4656718	0.89[ASW][hapmap]
rs4656720	0.93[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656722	0.93[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656723	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4656726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656727	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656732	1.00[CEU][hapmap]
rs55806711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57805301	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58111285	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60191157	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60315765	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61806076	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61807812	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61807813	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61807814	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61807817	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61807818	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61807835	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61807840	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73026253	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
9	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:169833800-169860200	Weak transcription	HMEC	breast
12	chr1:169841800-169848400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:169841800-169848400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:169841800-169848600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:169841800-169848600	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:169842000-169848400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:169842000-169848400	Strong transcription	Fetal Thymus	thymus
18	chr1:169842000-169848600	Strong transcription	Fetal Intestine Large	intestine
19	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
20	chr1:169842400-169848400	Strong transcription	Dnd41	blood
21	chr1:169842400-169848800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
23	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:169843000-169850200	Weak transcription	Colonic Mucosa	Colon
29	chr1:169843000-169851000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:169843200-169848600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:169843600-169848400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:169843600-169855000	Weak transcription	NHEK	skin
33	chr1:169843800-169848600	Strong transcription	Primary T cells from cord blood	blood
34	chr1:169843800-169850800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:169844000-169851200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:169844000-169851200	Weak transcription	Pancreas	Pancrea
37	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:169844400-169857400	Weak transcription	K562	blood
39	chr1:169844800-169851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:169844800-169854600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:169844800-169855400	Weak transcription	Hela-S3	cervix
42	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:169845000-169854000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:169845200-169850800	Weak transcription	Brain Germinal Matrix	brain
46	chr1:169845200-169850800	Weak transcription	Lung	lung
47	chr1:169845200-169851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:169845200-169851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:169845200-169853800	Weak transcription	Fetal Kidney	kidney
50	chr1:169845200-169854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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