Variant report

Variant	rs781663
Chromosome Location	chr4:57781754-57781755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57772971..57776902-chr4:57777481..57784789,10	MCF-7	breast:
2	chr4:57773013..57775637-chr4:57781437..57784341,3	MCF-7	breast:
3	chr4:57774412..57776864-chr4:57776976..57782053,6	K562	blood:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12645070	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17081933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17081935	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17087335	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2170073	0.87[JPT][hapmap]
rs2227901	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3733309	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs3796529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4339274	0.87[JPT][hapmap]
rs4412049	0.83[AMR][1000 genomes]
rs4560473	0.87[JPT][hapmap]
rs55762216	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55879786	0.83[EUR][1000 genomes]
rs56155140	0.86[EUR][1000 genomes]
rs56162812	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56281640	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57265257	0.85[EUR][1000 genomes]
rs58408429	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58548607	0.83[AMR][1000 genomes]
rs59713092	0.83[AMR][1000 genomes]
rs6554401	0.85[EUR][1000 genomes]
rs66790703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67043033	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6852182	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6852997	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6853156	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72606404	0.85[EUR][1000 genomes]
rs72627508	0.85[EUR][1000 genomes]
rs72627509	0.83[EUR][1000 genomes]
rs73165958	0.83[AMR][1000 genomes]
rs73165962	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73165963	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73165969	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7658601	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665147	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687767	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs781656	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs781657	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs781658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 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	chr4:57775800-57786200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57776400-57784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr4:57776400-57789400	Weak transcription	Right Ventricle	heart
4	chr4:57777000-57784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:57777000-57785400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr4:57777000-57786400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:57777000-57795800	Weak transcription	A549	lung
8	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
9	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:57777200-57793400	Weak transcription	HMEC	breast
11	chr4:57777200-57796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:57777200-57796600	Weak transcription	Aorta	Aorta
13	chr4:57777200-57796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:57777200-57797200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:57777400-57784600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:57777400-57786200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:57777600-57782000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:57777600-57783200	Weak transcription	Osteobl	bone
19	chr4:57777600-57784000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:57777600-57785800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:57777600-57796000	Weak transcription	Brain Anterior Caudate	brain
22	chr4:57777600-57796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:57777600-57796600	Weak transcription	Colonic Mucosa	Colon
24	chr4:57777600-57803200	Weak transcription	NHDF-Ad	bronchial
25	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:57778000-57781800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:57778000-57781800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:57778000-57785600	Strong transcription	Fetal Stomach	stomach
30	chr4:57778000-57791800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:57778000-57796000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:57778000-57796000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:57778000-57796600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:57778000-57797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:57778200-57781800	Weak transcription	Hela-S3	cervix
36	chr4:57778200-57783000	Weak transcription	Brain Substantia Nigra	brain
37	chr4:57778200-57783000	Weak transcription	K562	blood
38	chr4:57778200-57784000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:57778200-57784000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr4:57778200-57784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:57778200-57785600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:57778200-57796200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:57778200-57796800	Weak transcription	NHLF	lung
44	chr4:57778400-57781800	Weak transcription	Fetal Heart	heart
45	chr4:57778400-57781800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr4:57778400-57783600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:57778400-57784400	Weak transcription	NH-A	brain
48	chr4:57778400-57786200	Weak transcription	HSMM	muscle
49	chr4:57778400-57788600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:57778400-57795400	Weak transcription	HSMMtube	muscle

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