Variant report

Variant	rs11579402
Chromosome Location	chr1:180081856-180081857
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179833274..179835452-chr1:180080755..180083223,2	K562	blood:
2	chr1:180080477..180082075-chr1:180121926..180124694,2	MCF-7	breast:
3	chr1:180081238..180084639-chr1:180085491..180090263,5	K562	blood:
4	chr1:180081592..180084164-chr1:180086983..180088738,2	K562	blood:
5	chr1:180078830..180083672-chr1:180084739..180086615,4	K562	blood:

Variant related genes	Relation type
ENSG00000116260	Chromatin interaction
ENSG00000258664	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10798731	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10798733	1.00[ASN][1000 genomes]
rs10913911	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913912	1.00[ASN][1000 genomes]
rs10913913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs10913921	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10913922	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913928	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12117957	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12119113	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120822	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12124175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs12124336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127248	1.00[ASN][1000 genomes]
rs12129928	1.00[ASN][1000 genomes]
rs12131995	1.00[ASN][1000 genomes]
rs12135952	1.00[ASN][1000 genomes]
rs12137562	1.00[CHB][hapmap]
rs12138251	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144757	1.00[ASN][1000 genomes]
rs12743903	1.00[ASN][1000 genomes]
rs12744192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3845390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4083553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4652477	1.00[ASN][1000 genomes]
rs4652478	1.00[ASN][1000 genomes]
rs55676403	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55882713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166206	1.00[ASN][1000 genomes]
rs58121876	1.00[ASN][1000 genomes]
rs59953116	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61605706	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425605	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72710619	1.00[ASN][1000 genomes]
rs72710658	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521701	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7521873	1.00[ASN][1000 genomes]
rs7522347	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533903	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538086	1.00[ASN][1000 genomes]
rs7539784	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555418	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425484	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425864	1.00[ASN][1000 genomes]
rs9425869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 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	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:180040800-180082200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr1:180042000-180082600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:180048800-180082200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr1:180052800-180082600	Strong transcription	Fetal Thymus	thymus
9	chr1:180052800-180085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:180053000-180083000	Strong transcription	Liver	Liver
11	chr1:180054000-180082600	Strong transcription	Dnd41	blood
12	chr1:180057600-180082600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:180057600-180082800	Strong transcription	Adipose Nuclei	Adipose
14	chr1:180066200-180082200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:180068800-180082000	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:180069200-180082000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:180069400-180082400	Strong transcription	Primary T cells from cord blood	blood
18	chr1:180071400-180084400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:180071800-180085000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:180073400-180082200	Strong transcription	Fetal Intestine Large	intestine
21	chr1:180073600-180082200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:180073800-180083000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:180073800-180084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:180074000-180082400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:180074200-180082200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:180074200-180082400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:180074200-180083000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:180075800-180082200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:180077200-180082200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:180077400-180082200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr1:180077400-180082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:180077800-180082000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:180077800-180082400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:180078000-180082200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:180078000-180082200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:180078000-180082200	Strong transcription	Placenta	Placenta
37	chr1:180078000-180082200	Strong transcription	Osteobl	bone
38	chr1:180078000-180082400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:180078600-180082200	Strong transcription	Brain Angular Gyrus	brain
40	chr1:180078600-180082200	Strong transcription	Thymus	Thymus
41	chr1:180078600-180082400	Strong transcription	GM12878-XiMat	blood
42	chr1:180078600-180082600	Strong transcription	Left Ventricle	heart
43	chr1:180078600-180083400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:180078600-180084800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:180079000-180082200	Strong transcription	Hela-S3	cervix
46	chr1:180079000-180082400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:180079200-180082200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:180079200-180082200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:180079200-180082200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:180079200-180082200	Strong transcription	NH-A	brain

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