Variant report

Variant	rs11211340
Chromosome Location	chr1:47153855-47153856
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47131372..47133587-chr1:47151853..47154733,2	MCF-7	breast:
2	chr1:47151853..47154363-chr1:47155084..47157704,2	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000233647	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10890409	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890412	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890413	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211334	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211339	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211351	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1139759	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026027	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12029031	0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038572	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118483	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138338	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12142631	0.83[EUR][1000 genomes]
rs12733214	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440484	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007344	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083486	0.87[JPT][hapmap]
rs2218190	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737729	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660950	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660957	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs620913	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
4	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
7	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
9	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:47140000-47155400	Strong transcription	HSMM	muscle
13	chr1:47141200-47157800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:47142000-47159400	Strong transcription	K562	blood
16	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:47142400-47158000	Strong transcription	HMEC	breast
18	chr1:47142600-47158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
20	chr1:47142600-47159400	Strong transcription	NHEK	skin
21	chr1:47142800-47158800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:47143600-47158400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:47143800-47158200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
33	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:47144000-47158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:47145000-47158000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:47145400-47158000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:47145400-47159000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:47145600-47157800	Strong transcription	NH-A	brain
40	chr1:47145800-47155800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:47145800-47158800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:47147000-47158200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:47147600-47158400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:47147800-47155800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:47147800-47157200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:47148000-47158000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:47148000-47158200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:47148000-47158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:47148400-47159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:47148800-47159400	Strong transcription	Hela-S3	cervix

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