Variant report

Variant	rs1994090
Chromosome Location	chr12:40428561-40428562
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40427544..40429854-chr12:40484526..40486904,2	MCF-7	breast:
2	chr12:40428243..40430877-chr12:40432067..40435027,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1384234	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs1384236	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1463718	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs1482289	0.91[ASN][1000 genomes]
rs1491933	1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs17458501	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2708446	0.91[ASN][1000 genomes]
rs2708453	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs4768210	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4768212	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7134524	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs7304279	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7306944	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7315459	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7978715	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Parkinson's disease	19915576	GWAS catalog

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:40416600-40441800	Weak transcription	Ovary	ovary
5	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
6	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
7	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
8	chr12:40425200-40429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:40425400-40429200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:40425600-40429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:40425600-40429800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:40426000-40428800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:40426000-40429000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr12:40426200-40429000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:40426800-40429000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:40427000-40429200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:40427200-40429000	Enhancers	Stomach Mucosa	stomach
19	chr12:40427800-40428800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:40427800-40429200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:40427800-40430000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:40428000-40429000	Enhancers	Fetal Lung	lung
23	chr12:40428000-40429000	Enhancers	NHDF-Ad	bronchial
24	chr12:40428000-40429400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:40428000-40429600	Enhancers	A549	lung
26	chr12:40428000-40436400	Weak transcription	Fetal Intestine Large	intestine
27	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:40428200-40428600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:40428200-40428800	Enhancers	Brain Germinal Matrix	brain
30	chr12:40428200-40428800	Enhancers	Osteobl	bone

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