Variant report

Variant	rs2420511
Chromosome Location	chr1:169812583-169812584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169811782..169814022-chr1:169814299..169816027,2	MCF-7	breast:
2	chr1:169812131..169813776-chr1:169822514..169824878,2	K562	blood:
3	chr1:169764137..169766860-chr1:169812488..169814041,2	K562	blood:
4	chr1:169790924..169793172-chr1:169810739..169813413,2	K562	blood:
5	chr1:169810189..169813776-chr1:169821630..169824014,3	K562	blood:
6	chr1:169812533..169814235-chr1:169854142..169856140,2	MCF-7	breast:
7	chr1:169810204..169812691-chr1:169819466..169821386,2	MCF-7	breast:
8	chr1:169811782..169814669-chr1:169816752..169818969,2	K562	blood:

No data

Variant related genes	Relation type
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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11578817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579102	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]
rs11579709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11581959	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11582552	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap]
rs11585093	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11589659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572551	1.00[CEU][hapmap]
rs16828209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16862705	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862902	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs1928887	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs2420510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34657513	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35196850	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3753312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766150	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817859	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]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4656198	0.89[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4656201	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656722	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656723	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656732	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs55806711	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57805301	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58111285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60191157	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60315765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807812	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61807813	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61807814	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61807817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61807818	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61807835	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61807840	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73026253	0.82[AMR][1000 genomes];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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
2	chr1:169764800-169818200	Weak transcription	Lung	lung
3	chr1:169764800-169823600	Weak transcription	Gastric	stomach
4	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
9	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
10	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
11	chr1:169765600-169818200	Weak transcription	NHLF	lung
12	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:169784000-169814000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:169784000-169814800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:169786600-169841400	Strong transcription	Dnd41	blood
19	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
20	chr1:169789200-169818600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
22	chr1:169793800-169814400	Weak transcription	Brain Substantia Nigra	brain
23	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:169794000-169814800	Weak transcription	Aorta	Aorta
25	chr1:169794200-169818400	Weak transcription	NHEK	skin
26	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:169797000-169818200	Weak transcription	Spleen	Spleen
28	chr1:169797600-169818200	Weak transcription	HSMMtube	muscle
29	chr1:169797800-169813400	Weak transcription	Fetal Intestine Large	intestine
30	chr1:169799200-169814800	Weak transcription	Osteobl	bone
31	chr1:169799400-169814800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:169800000-169814800	Weak transcription	HMEC	breast
33	chr1:169802200-169812800	Weak transcription	NH-A	brain
34	chr1:169802200-169822600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:169802400-169821800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:169802600-169813000	Weak transcription	Left Ventricle	heart
37	chr1:169802800-169815000	Weak transcription	Hela-S3	cervix
38	chr1:169802800-169819800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:169803000-169813000	Weak transcription	Ovary	ovary
40	chr1:169804200-169812800	Weak transcription	HepG2	liver
41	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:169806400-169813400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:169806400-169820600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
45	chr1:169807000-169816600	Weak transcription	NHDF-Ad	bronchial
46	chr1:169808000-169815200	Weak transcription	Fetal Stomach	stomach
47	chr1:169808200-169812800	Weak transcription	A549	lung
48	chr1:169808200-169819800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:169808200-169822000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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