Variant report

Variant	rs12692423
Chromosome Location	chr2:11075317-11075318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11053891..11056006-chr2:11074074..11075819,2	MCF-7	breast:
2	chr2:11074983..11076503-chr2:11504797..11506450,2	MCF-7	breast:
3	chr2:11074723..11077921-chr2:11081034..11085033,4	MCF-7	breast:
4	chr2:11050815..11054618-chr2:11074174..11077815,3	MCF-7	breast:
5	chr2:11063866..11066911-chr2:11073875..11076596,3	K562	blood:
6	chr2:11049420..11051539-chr2:11073823..11076217,2	MCF-7	breast:
7	chr2:11075163..11076703-chr2:11081992..11083807,2	K562	blood:
8	chr2:11073057..11076699-chr2:11262086..11264690,5	MCF-7	breast:
9	chr2:11051753..11053643-chr2:11073602..11075521,2	MCF-7	breast:
10	chr2:11070868..11073523-chr2:11073573..11076580,4	MCF-7	breast:
11	chr2:11074952..11076639-chr2:11264485..11265994,2	MCF-7	breast:
12	chr2:11065411..11067104-chr2:11075096..11077076,2	K562	blood:
13	chr2:11063730..11067649-chr2:11070741..11076086,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162975	Chromatin interaction
ENSG00000230952	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12692424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453083	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1453087	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs1453088	0.90[ASN][1000 genomes]
rs17365719	0.90[ASN][1000 genomes]
rs4669647	0.90[CHB][hapmap]
rs930763	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580969	chr2:11033567-11081645	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv833392	chr2:11054580-11235239	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv817618	chr2:11055298-11075754	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv469438	chr2:11055298-11085744	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv580970	chr2:11055298-11085744	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv523537	chr2:11061156-11075317	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11066800-11075400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:11070600-11078400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:11070800-11077000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:11070800-11077600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:11071000-11076200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:11071800-11076400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:11072400-11077400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:11072800-11076600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:11072800-11077000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:11073200-11075400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:11073600-11076200	Weak transcription	Fetal Kidney	kidney
12	chr2:11073800-11075800	Weak transcription	Lung	lung
13	chr2:11073800-11075800	Bivalent Enhancer	HepG2	liver
14	chr2:11074000-11075400	Weak transcription	Osteobl	bone
15	chr2:11074200-11076000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr2:11074200-11077400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:11074400-11076600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:11074400-11076800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:11074400-11077000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:11074400-11077000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:11074400-11077400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:11074400-11077400	Enhancers	NH-A	brain
23	chr2:11074600-11075400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:11074600-11075400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:11074600-11075800	Enhancers	Fetal Brain Male	brain
26	chr2:11074600-11075800	Enhancers	Fetal Muscle Leg	muscle
27	chr2:11074600-11075800	Bivalent Enhancer	Fetal Stomach	stomach
28	chr2:11074600-11076400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:11074600-11076600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:11074600-11076800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:11074600-11076800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:11074600-11076800	Enhancers	Fetal Lung	lung
33	chr2:11074600-11077000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:11074600-11077400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:11074800-11075800	Enhancers	Brain Germinal Matrix	brain
36	chr2:11074800-11076000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr2:11074800-11077400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:11075000-11075400	Bivalent Enhancer	Placenta	Placenta
39	chr2:11075000-11075600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr2:11075000-11075600	Enhancers	Spleen	Spleen
41	chr2:11075000-11076600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:11075000-11077400	Enhancers	NHDF-Ad	bronchial
43	chr2:11075000-11077400	Enhancers	NHLF	lung
44	chr2:11075000-11077600	Enhancers	HUVEC	blood vessel
45	chr2:11075200-11075400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:11075200-11075400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:11075200-11075600	Enhancers	Brain Angular Gyrus	brain
48	chr2:11075200-11076000	Flanking Active TSS	A549	lung
49	chr2:11075200-11076800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:11075200-11077000	Enhancers	HMEC	breast

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