Variant report

Variant	rs11892004
Chromosome Location	chr2:47306991-47306992
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47305124..47307804-chr2:47314133..47316358,4	MCF-7	breast:
2	chr2:47303169..47307562-chr2:47312603..47317235,6	MCF-7	breast:
3	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
4	chr2:47304999..47307834-chr2:47310076..47312199,2	MCF-7	breast:
5	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
6	chr2:47304449..47306633-chr2:47306977..47308538,2	MCF-7	breast:
7	chr2:47297108..47300673-chr2:47304396..47307131,4	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2280646	0.81[TSI][hapmap]
rs6723182	0.82[ASN][1000 genomes]
rs7569336	0.85[ASN][1000 genomes]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11892004	SIX3	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47300600-47310400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:47301600-47307200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:47302000-47307200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:47302000-47307400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:47302200-47307400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:47302200-47308400	Enhancers	Lung	lung
7	chr2:47302400-47307600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:47302400-47307600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:47302400-47308400	Enhancers	Placenta	Placenta
10	chr2:47302600-47307400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:47302600-47307600	Enhancers	NHDF-Ad	bronchial
12	chr2:47302600-47308400	Enhancers	Stomach Mucosa	stomach
13	chr2:47302800-47307000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:47302800-47308200	Enhancers	Colonic Mucosa	Colon
15	chr2:47303200-47307000	Weak transcription	Fetal Brain Female	brain
16	chr2:47303200-47308400	Enhancers	Pancreas	Pancrea
17	chr2:47303400-47308800	Enhancers	Adipose Nuclei	Adipose
18	chr2:47303600-47307600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr2:47303800-47308400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:47304200-47310800	Weak transcription	Primary B cells from cord blood	blood
21	chr2:47304400-47307600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:47304800-47307400	Weak transcription	Primary T cells from cord blood	blood
23	chr2:47305000-47307000	Enhancers	Spleen	Spleen
24	chr2:47305000-47307200	Enhancers	K562	blood
25	chr2:47305000-47307600	Enhancers	HSMM	muscle
26	chr2:47305200-47307000	Weak transcription	Thymus	Thymus
27	chr2:47305200-47310000	Weak transcription	HMEC	breast
28	chr2:47305400-47307000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:47305400-47307600	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:47305600-47307600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:47305600-47307800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:47305600-47308400	Enhancers	Fetal Intestine Large	intestine
33	chr2:47305800-47307200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr2:47305800-47307200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:47305800-47307200	Flanking Active TSS	Liver	Liver
36	chr2:47305800-47307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:47305800-47307400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:47305800-47307600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:47305800-47307600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:47305800-47307600	Enhancers	Brain Substantia Nigra	brain
41	chr2:47305800-47307600	Flanking Active TSS	HepG2	liver
42	chr2:47305800-47307600	Enhancers	NH-A	brain
43	chr2:47305800-47307800	Enhancers	Left Ventricle	heart
44	chr2:47305800-47307800	Enhancers	Right Atrium	heart
45	chr2:47305800-47308200	Enhancers	Brain Anterior Caudate	brain
46	chr2:47305800-47308400	Enhancers	Brain Hippocampus Middle	brain
47	chr2:47305800-47310200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:47306000-47307000	Enhancers	Fetal Intestine Small	intestine
49	chr2:47306000-47307200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:47306000-47307200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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