Variant report

Variant	rs833480
Chromosome Location	chr12:49278861-49278862
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49246388..49252218-chr12:49276087..49280065,7	MCF-7	breast:
2	chr12:49275956..49279461-chr12:49283300..49286531,4	MCF-7	breast:
3	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
4	chr12:49273861..49275618-chr12:49278332..49280043,2	MCF-7	breast:
5	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
6	chr12:49276917..49280280-chr12:49283219..49286162,3	K562	blood:
7	chr12:49250519..49252141-chr12:49277437..49280181,2	MCF-7	breast:
8	chr12:49265197..49267414-chr12:49276769..49280973,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199394	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10783288	1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs10875884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17175174	1.00[JPT][hapmap]
rs1874275	0.86[EUR][1000 genomes]
rs2228417	1.00[JPT][hapmap]
rs2453477	1.00[JPT][hapmap]
rs7954041	0.87[AFR][1000 genomes]
rs833474	0.94[AFR][1000 genomes]
rs833475	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833477	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs833482	1.00[JPT][hapmap]
rs872313	0.89[GIH][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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs833480	AQP6	cis	cerebellum	SCAN
rs833480	ARID2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49277400-49279600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:49277800-49283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:49277800-49284800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:49278000-49280200	Weak transcription	Gastric	stomach
5	chr12:49278000-49280800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:49278000-49284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:49278000-49284400	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:49278200-49279000	Enhancers	A549	lung
9	chr12:49278200-49279600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:49278200-49280200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:49278200-49280200	Weak transcription	Fetal Intestine Large	intestine
12	chr12:49278200-49280800	Weak transcription	K562	blood
13	chr12:49278200-49281200	Enhancers	HepG2	liver
14	chr12:49278200-49283400	Weak transcription	Brain Germinal Matrix	brain
15	chr12:49278200-49284200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:49278200-49284200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:49278200-49284400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:49278400-49280000	Weak transcription	Stomach Mucosa	stomach
19	chr12:49278400-49283800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:49278400-49283800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:49278400-49284000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:49278400-49284600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:49278600-49281000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:49278800-49283600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:49278800-49284200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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