Variant report

Variant	rs7654466
Chromosome Location	chr4:48177776-48177777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48177121..48180289-chr4:48181668..48184747,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10016563	1.00[ASN][1000 genomes]
rs12331972	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470892	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471024	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17574371	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521484	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28702422	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28740900	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809586	1.00[ASN][1000 genomes]
rs6814046	0.80[EUR][1000 genomes]
rs6814614	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684558	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996222	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1006853	chr4:48164958-48196335	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1011820	chr4:48170669-48186729	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv819982	chr4:48173420-48178259	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1011366	chr4:48173947-48186644	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1005668	chr4:48173947-48186729	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48157800-48181000	Weak transcription	Pancreas	Pancrea
2	chr4:48158400-48180600	Weak transcription	Spleen	Spleen
3	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
5	chr4:48158600-48179200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:48158600-48179400	Weak transcription	Fetal Intestine Small	intestine
7	chr4:48158800-48180200	Weak transcription	Fetal Thymus	thymus
8	chr4:48166400-48179600	Weak transcription	Thymus	Thymus
9	chr4:48169000-48180600	Weak transcription	Esophagus	oesophagus
10	chr4:48169000-48190000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:48170600-48181200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:48171200-48181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:48173800-48188400	Weak transcription	Lung	lung
14	chr4:48174400-48178000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:48175400-48178800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:48175600-48178000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:48175600-48180600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:48175800-48191600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:48176000-48178400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:48176000-48180600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:48176000-48185200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:48176000-48185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:48176000-48185400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:48176200-48185200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:48176600-48179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:48176800-48177800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:48176800-48178000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr4:48176800-48178000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:48177000-48178200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr4:48177000-48178200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:48177000-48178200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:48177000-48178200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:48177200-48178000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:48177200-48178200	Enhancers	HUVEC	blood vessel
35	chr4:48177400-48177800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:48177400-48177800	Enhancers	Hela-S3	cervix
37	chr4:48177400-48178000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:48177400-48178000	Enhancers	Primary T cells from cord blood	blood
39	chr4:48177400-48178000	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr4:48177400-48178200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:48177400-48178200	Enhancers	A549	lung
42	chr4:48177400-48178200	Enhancers	HMEC	breast
43	chr4:48177400-48178200	Enhancers	NH-A	brain
44	chr4:48177400-48178200	Enhancers	NHEK	skin
45	chr4:48177400-48179400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:48177600-48177800	Weak transcription	K562	blood
47	chr4:48177600-48178000	Genic enhancers	GM12878-XiMat	blood
48	chr4:48177600-48178200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr4:48177600-48179200	Weak transcription	Liver	Liver
50	chr4:48177600-48182200	Weak transcription	HSMM	muscle

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