Variant report

Variant	rs190148089
Chromosome Location	chr3:160822123-160822124
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr3:160822071-160823714	MCF-7	breast:	n/a	n/a
2	MAX	chr3:160821640-160823909	MCF-7	breast:	n/a	n/a
3	E2F6	chr3:160822061-160823742	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
4	HDAC2	chr3:160821953-160823716	MCF-7	breast:	n/a	n/a
5	REST	chr3:160822099-160822792	H1-neurons	neurons:	n/a	n/a
6	BRCA1	chr3:160822109-160822390	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160819969..160822199-chr3:161125222..161127254,2	MCF-7	breast:
3	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
4	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GALNT1-1	chr3:160822107-160822194	NONHSAT093005
2	lnc-B3GALNT1-1	chr3:160822107-160822194	NONHSAT093006
3	lnc-B3GALNT1-1	chr3:160822107-160822194	NONHSAT093007
4	lnc-B3GALNT1-1	chr3:160822107-160822194	NONHSAT093008
5	lnc-B3GALNT1-1	chr3:160822107-160822194	NONHSAT093009

No data

Variant related genes	Relation type
B3GALNT1	TF binding region
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3420135	chr3:160821883-160824431	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
3	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:160804600-160822200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160809000-160822200	Weak transcription	Psoas Muscle	Psoas
6	chr3:160816000-160822200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:160819000-160822200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:160819400-160822200	Weak transcription	Gastric	stomach
9	chr3:160820000-160822200	Weak transcription	Placenta	Placenta
10	chr3:160821400-160822200	Flanking Active TSS	Fetal Heart	heart
11	chr3:160821600-160822200	Enhancers	Pancreas	Pancrea
12	chr3:160821600-160823200	Active TSS	Right Ventricle	heart
13	chr3:160821800-160822200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:160821800-160822200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:160821800-160822200	Active TSS	Brain Germinal Matrix	brain
16	chr3:160821800-160822200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr3:160821800-160822200	Enhancers	Stomach Mucosa	stomach
18	chr3:160821800-160822200	Flanking Active TSS	Osteobl	bone
19	chr3:160821800-160822400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr3:160821800-160823200	Active TSS	Left Ventricle	heart
21	chr3:160821800-160823600	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:160821800-160823600	Active TSS	Fetal Brain Female	brain
23	chr3:160821800-160823600	Active TSS	Stomach Smooth Muscle	stomach
24	chr3:160821800-160823800	Active TSS	Brain Substantia Nigra	brain
25	chr3:160821800-160824200	Active TSS	Fetal Kidney	kidney
26	chr3:160822000-160822200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:160822000-160822200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:160822000-160822200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:160822000-160822200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:160822000-160822200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:160822000-160822200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
32	chr3:160822000-160822200	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:160822000-160822200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:160822000-160822200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:160822000-160822200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:160822000-160822200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:160822000-160822200	Enhancers	Liver	Liver
38	chr3:160822000-160822200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr3:160822000-160822200	Flanking Active TSS	Fetal Intestine Large	intestine
40	chr3:160822000-160822200	Flanking Active TSS	Fetal Lung	lung
41	chr3:160822000-160822200	Flanking Active TSS	Fetal Stomach	stomach
42	chr3:160822000-160822200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:160822000-160822200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
44	chr3:160822000-160822200	Enhancers	Thymus	Thymus
45	chr3:160822000-160822200	Flanking Active TSS	NHDF-Ad	bronchial
46	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
49	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr3:160822000-160822400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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