Variant report

Variant	rs559737571
Chromosome Location	chr3:138544269-138544270
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	chr3:138544244..138546193-chr3:138552425..138554988,2	MCF-7	breast:
2	chr3:138541276..138545209-chr3:138550830..138554565,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf72-4	chr3:138543905-138545171	NONHSAT092341

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv967072	chr3:138543196-138550847	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138504000-138552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:138506000-138551800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:138513400-138544400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:138528800-138552600	Weak transcription	Colonic Mucosa	Colon
5	chr3:138529400-138544400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:138535200-138551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:138537000-138552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:138537200-138548400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:138537200-138552000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:138537200-138552200	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:138537400-138544400	Weak transcription	Spleen	Spleen
12	chr3:138537400-138551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:138537400-138552200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:138537600-138544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:138537600-138544400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:138537600-138549000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:138537600-138551200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:138537600-138551400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:138537600-138551400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:138537600-138552000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:138537600-138552200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:138537600-138552200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:138537600-138552400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:138537600-138552400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:138537600-138552600	Weak transcription	Ovary	ovary
26	chr3:138538000-138544400	Weak transcription	Psoas Muscle	Psoas
27	chr3:138538200-138544400	Weak transcription	Lung	lung
28	chr3:138539200-138551200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:138539200-138552200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:138539400-138544600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:138539400-138544600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:138540600-138545600	Weak transcription	Brain Germinal Matrix	brain
33	chr3:138541400-138544400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:138542600-138544400	Enhancers	Fetal Heart	heart
35	chr3:138542600-138544400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:138542800-138544400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:138542800-138544600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:138543000-138544800	Genic enhancers	HepG2	liver
39	chr3:138543000-138545200	Genic enhancers	K562	blood
40	chr3:138543000-138546000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:138543000-138552200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:138543200-138544400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:138543200-138544400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:138543200-138545000	Strong transcription	Thymus	Thymus
45	chr3:138543200-138552200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:138543200-138552400	Weak transcription	Fetal Stomach	stomach
47	chr3:138543400-138544400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:138543400-138544400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:138543400-138544400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr3:138543400-138544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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