Variant report

Variant	rs3796860
Chromosome Location	chr4:15977823-15977824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15695760..15698048-chr4:15975957..15978418,2	MCF-7	breast:
2	chr4:15976147..15979142-chr4:16221984..16223628,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10488967	0.87[EUR][1000 genomes]
rs11725522	0.91[EUR][1000 genomes]
rs3796858	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796861	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796862	0.99[EUR][1000 genomes]
rs6833237	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855282	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669462	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9685105	0.88[AMR][1000 genomes];0.91[EUR][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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv980121	chr4:15976687-15978027	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15940200-15983600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:15965200-15983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:15965400-15979000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:15965600-15984000	Weak transcription	Colonic Mucosa	Colon
6	chr4:15967800-15983600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:15968000-16002600	Weak transcription	Left Ventricle	heart
8	chr4:15968200-15978200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:15968600-15979600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:15968600-15993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:15968800-15983600	Weak transcription	Pancreas	Pancrea
12	chr4:15968800-15992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:15969600-15990000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
15	chr4:15969800-15986200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:15971000-15978200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:15971000-15983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:15971000-15992200	Weak transcription	Fetal Brain Male	brain
19	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
20	chr4:15971200-15979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:15973200-15980000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:15973200-15993800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:15973600-15978200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:15973800-15978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:15973800-15979000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:15974000-15991800	Weak transcription	Fetal Intestine Small	intestine
27	chr4:15974400-15978200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:15974400-15979600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:15974600-15980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:15975000-15978200	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:15975000-15978200	Weak transcription	Fetal Stomach	stomach
32	chr4:15975600-15978400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:15976400-15982000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:15976400-15985800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:15976600-15984400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:15976800-16002600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:15977000-16007400	Weak transcription	Gastric	stomach
38	chr4:15977200-15981000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:15977600-15982200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:15977800-15978600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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