Variant report

Variant	rs1868172
Chromosome Location	chr3:139493701-139493702
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	chr3:139491615..139494435-chr3:139496230..139498202,2	MCF-7	breast:
2	chr3:139493162..139494985-chr3:139496396..139498137,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11708516	0.95[ASN][1000 genomes]
rs11710391	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11921293	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11921303	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17315928	0.84[ASN][1000 genomes]
rs17393618	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17393660	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17393848	0.96[ASN][1000 genomes]
rs56161455	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59161850	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59549192	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60101099	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62270255	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62270256	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62271861	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772801	0.97[ASN][1000 genomes]
rs72975869	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430535	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs765193	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765194	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139481600-139496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:139488400-139494000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:139490000-139495000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:139490000-139495200	Enhancers	Fetal Muscle Leg	muscle
5	chr3:139490200-139495600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:139490800-139494000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:139490800-139494000	Enhancers	NHDF-Ad	bronchial
8	chr3:139491000-139494000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:139491200-139493800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:139491600-139494000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:139492200-139494000	Enhancers	Ovary	ovary
12	chr3:139492400-139494600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:139492600-139494000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:139492600-139494000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:139492800-139494000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:139492800-139494000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:139492800-139494000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:139492800-139494000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:139492800-139494000	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:139492800-139494000	Enhancers	Psoas Muscle	Psoas
21	chr3:139492800-139494000	Enhancers	Right Atrium	heart
22	chr3:139492800-139494200	Enhancers	Brain Germinal Matrix	brain
23	chr3:139492800-139494200	Enhancers	Fetal Brain Male	brain
24	chr3:139492800-139494400	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:139493000-139493800	Enhancers	Pancreas	Pancrea
26	chr3:139493000-139494000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:139493000-139494000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr3:139493000-139494000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:139493000-139494000	Enhancers	Adipose Nuclei	Adipose
30	chr3:139493000-139494000	Enhancers	Brain Hippocampus Middle	brain
31	chr3:139493200-139494000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:139493200-139494000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:139493200-139494000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:139493200-139494000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:139493200-139494000	Enhancers	Fetal Stomach	stomach
36	chr3:139493400-139493800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:139493400-139493800	Enhancers	Brain Anterior Caudate	brain
38	chr3:139493400-139493800	Enhancers	HSMM	muscle
39	chr3:139493400-139493800	Enhancers	NH-A	brain
40	chr3:139493400-139494000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:139493400-139494000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr3:139493400-139494000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr3:139493400-139494000	Enhancers	Fetal Brain Female	brain
44	chr3:139493400-139495400	Enhancers	HSMMtube	muscle
45	chr3:139493600-139493800	Enhancers	Skeletal Muscle Male	skeletal muscle

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