Variant report

Variant	rs3812047
Chromosome Location	chr5:37835398-37835399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr5:37834965-37835413	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr5:37834547-37835407	H1-hESC	embryonic stem cell:	n/a	chr5:37834578-37834590 chr5:37835018-37835030 chr5:37834576-37834589 chr5:37835246-37835265
3	CTBP2	chr5:37834793-37835438	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr5:37834588-37835735	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37834038..37837439-chr5:37839505..37841588,3	MCF-7	breast:

Variant related genes	Relation type
GDNF	TF binding region
ENSG00000248587	Chromatin interaction
ENSG00000168621	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11749171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951867	0.83[CEU][hapmap]
rs16903732	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs17386472	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs949859	0.81[CEU][hapmap]

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	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv1844348	chr5:37835398-37840642	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1851519	chr5:37835398-37840642	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37833400-37836600	Weak transcription	NHEK	skin
2	chr5:37833800-37835400	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr5:37834000-37835400	Bivalent Enhancer	Fetal Heart	heart
4	chr5:37834200-37835600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:37834200-37836600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
6	chr5:37834200-37837800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr5:37834200-37838200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr5:37834200-37838400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr5:37834200-37839000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:37834200-37841000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:37834400-37835400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr5:37834400-37835400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr5:37834400-37835400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:37834400-37835400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:37834400-37835400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:37834400-37835400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
17	chr5:37834400-37835600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:37834400-37836000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:37834400-37836400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr5:37834400-37836800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:37834400-37836800	Bivalent Enhancer	Placenta	Placenta
22	chr5:37834400-37838800	Active TSS	Colon Smooth Muscle	Colon
23	chr5:37834400-37840600	Bivalent Enhancer	Fetal Brain Male	brain
24	chr5:37834400-37841400	Bivalent/Poised TSS	Colonic Mucosa	Colon
25	chr5:37834600-37835400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:37834600-37835400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr5:37834600-37835400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr5:37834600-37835400	Weak transcription	NHDF-Ad	bronchial
29	chr5:37834600-37835600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr5:37834600-37836200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr5:37834600-37836400	Weak transcription	HSMMtube	muscle
32	chr5:37834600-37836600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr5:37834600-37837800	Active TSS	Rectal Smooth Muscle	rectum
34	chr5:37834800-37835400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:37834800-37835400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:37834800-37835400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:37834800-37835400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:37834800-37835400	Bivalent Enhancer	Lung	lung
39	chr5:37834800-37835600	Bivalent Enhancer	Spleen	Spleen
40	chr5:37834800-37835600	Flanking Active TSS	NH-A	brain
41	chr5:37834800-37836800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr5:37835000-37835400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:37835000-37835400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:37835000-37835400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
45	chr5:37835000-37835400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
46	chr5:37835000-37835600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr5:37835000-37835600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
48	chr5:37835000-37835800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
49	chr5:37835000-37836000	Bivalent Enhancer	Fetal Brain Female	brain
50	chr5:37835000-37836600	Weak transcription	Right Atrium	heart

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