Variant report

Variant	rs10779456
Chromosome Location	chr1:221953057-221953058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221915140..221918678-chr1:221951678..221954670,3	K562	blood:
2	chr1:221950355..221953290-chr1:221957212..221959262,2	K562	blood:
3	chr1:221943490..221945963-chr1:221951979..221954121,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10218652	0.94[EUR][1000 genomes]
rs10495179	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10863653	0.92[EUR][1000 genomes]
rs10863654	0.94[EUR][1000 genomes]
rs10863655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863659	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11118847	0.86[EUR][1000 genomes]
rs11118848	0.92[CEU][hapmap]
rs11118854	0.92[EUR][1000 genomes]
rs11118857	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118860	1.00[CEU][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11118861	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11118862	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11118865	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11118866	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12070192	0.94[EUR][1000 genomes]
rs12076234	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12082239	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12083486	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12127111	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12136350	0.91[EUR][1000 genomes]
rs12144586	0.86[EUR][1000 genomes]
rs12145486	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12403995	0.84[EUR][1000 genomes]
rs17010720	0.94[EUR][1000 genomes]
rs3934724	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4073062	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4313407	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4433402	0.94[EUR][1000 genomes]
rs4589119	0.92[CEU][hapmap]
rs4601596	0.91[CEU][hapmap]
rs4623704	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55830234	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6655994	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6664523	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6687354	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7516292	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221947600-221953600	Weak transcription	Lung	lung
2	chr1:221948800-221955000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:221948800-221958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:221949000-221953800	Weak transcription	Adipose Nuclei	Adipose
5	chr1:221949000-221954600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:221949000-221955000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:221949200-221953400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:221949400-221958000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:221949600-221954800	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:221949600-221954800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:221949800-221953200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:221949800-221953800	Enhancers	Thymus	Thymus
13	chr1:221949800-221953800	Enhancers	Dnd41	blood
14	chr1:221949800-221954600	Enhancers	Primary T cells from cord blood	blood
15	chr1:221949800-221958200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:221950000-221954000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:221950000-221954400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:221950000-221956800	Enhancers	Fetal Thymus	thymus
19	chr1:221950600-221954400	Weak transcription	K562	blood
20	chr1:221950600-221955600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:221951400-221953200	Flanking Active TSS	GM12878-XiMat	blood
22	chr1:221951600-221954000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:221951800-221953600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:221951800-221958000	Enhancers	Primary B cells from cord blood	blood
25	chr1:221952000-221953400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr1:221952000-221953600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:221952000-221954000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:221952000-221954400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:221952000-221955000	Enhancers	Primary B cells from peripheral blood	blood
30	chr1:221952000-221958000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:221952400-221953600	Weak transcription	Spleen	Spleen
32	chr1:221952400-221953800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:221952400-221954000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:221952800-221953400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:221952800-221953400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:221953000-221953400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:221953000-221953800	Enhancers	Esophagus	oesophagus
38	chr1:221953000-221954600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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