Variant report

Variant	rs57720880
Chromosome Location	chr11:65851352-65851353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr11:65850665-65851495	SK-N-SH	brain:	n/a	chr11:65851056-65851065
2	NFIC	chr11:65850509-65851510	SK-N-SH	brain:	n/a	chr11:65851034-65851051
3	MXI1	chr11:65851051-65851365	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr11:65850441-65851513	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr11:65850439-65851412	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr11:65850723-65851353	MCF-7	breast:	n/a	n/a
7	KAP1	chr11:65850435-65851449	U2OS	brain:	n/a	n/a
8	TCF12	chr11:65850726-65851396	SK-N-SH	brain:	n/a	chr11:65851056-65851065
9	SIN3AK20	chr11:65850544-65851455	MCF-7	breast:	n/a	n/a
10	EP300	chr11:65850365-65851706	SK-N-SH	brain:	n/a	chr11:65851056-65851066
11	GATA3	chr11:65850549-65851467	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65850193..65852902-chr11:66111593..66113196,2	MCF-7	breast:
2	chr11:65849463..65852379-chr11:66024191..66026545,2	K562	blood:
3	chr1:145381411..145383817-chr11:65849842..65852203,2	MCF-7	breast:
4	chr11:65654594..65656480-chr11:65848880..65851795,2	K562	blood:

Variant related genes	Relation type
PACS1	TF binding region
ENSG00000233396	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000174744	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1211863	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452683	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930174	0.93[EUR][1000 genomes]
rs4930341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540943	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57287207	1.00[ASN][1000 genomes]
rs58583648	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59807152	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827057	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60095752	1.00[ASN][1000 genomes]
rs60415795	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591205	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591206	1.00[ASN][1000 genomes]
rs7103495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932629	1.00[ASN][1000 genomes]
rs72932698	1.00[ASN][1000 genomes]
rs72934614	0.93[EUR][1000 genomes]
rs72934624	0.93[EUR][1000 genomes]
rs72934632	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934636	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934642	0.93[EUR][1000 genomes]
rs72934655	0.93[EUR][1000 genomes]
rs72934666	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934668	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934673	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934677	0.93[EUR][1000 genomes]
rs72936625	0.89[EUR][1000 genomes]
rs7950327	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65839600-65854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:65840600-65870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:65842200-65867800	Weak transcription	Ovary	ovary
4	chr11:65842400-65851800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:65843600-65851400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:65845200-65854400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:65845800-65868800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:65846200-65853600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:65847200-65852000	Enhancers	Duodenum Mucosa	Duodenum
10	chr11:65847400-65851400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:65847400-65851600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr11:65847600-65851600	Enhancers	Small Intestine	intestine
13	chr11:65847600-65851600	Enhancers	NHDF-Ad	bronchial
14	chr11:65847600-65852000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:65847600-65852000	Enhancers	HUVEC	blood vessel
16	chr11:65847600-65852800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr11:65847600-65852800	Enhancers	Osteobl	bone
18	chr11:65847600-65853000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr11:65847800-65851600	Enhancers	HSMMtube	muscle
20	chr11:65848000-65851600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:65848000-65854800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65848200-65851400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:65848200-65851600	Weak transcription	Lung	lung
24	chr11:65848400-65874200	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:65848800-65851400	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:65849000-65853600	Enhancers	Fetal Heart	heart
27	chr11:65849200-65851400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:65849200-65852200	Enhancers	Hela-S3	cervix
29	chr11:65849200-65853400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:65849200-65879600	Weak transcription	Aorta	Aorta
31	chr11:65849400-65851400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:65849400-65851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:65849400-65851600	Enhancers	Thymus	Thymus
34	chr11:65849400-65852000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:65849400-65854600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:65849400-65856200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr11:65849400-65858000	Enhancers	Primary B cells from peripheral blood	blood
38	chr11:65849400-65858800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:65849600-65851600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr11:65849600-65852000	Enhancers	Fetal Thymus	thymus
41	chr11:65849600-65853400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:65849600-65856800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr11:65849600-65857000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:65849600-65858600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr11:65849800-65851400	Enhancers	Primary T cells from cord blood	blood
46	chr11:65849800-65851400	Enhancers	GM12878-XiMat	blood
47	chr11:65849800-65851600	Enhancers	Fetal Intestine Small	intestine
48	chr11:65849800-65853000	Enhancers	Primary hematopoietic stem cells	blood
49	chr11:65849800-65857800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr11:65849800-65858200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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