Variant report

Variant	rs12328197
Chromosome Location	chr2:47476877-47476878
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47462905..47465893-chr2:47474409..47477265,3	MCF-7	breast:
2	chr2:47471172..47473317-chr2:47476209..47479649,3	MCF-7	breast:
3	chr2:47473511..47478428-chr2:47483950..47488018,4	MCF-7	breast:
4	chr2:47475912..47477732-chr2:47481977..47484022,2	K562	blood:
5	chr2:47401347..47405305-chr2:47474858..47480763,8	MCF-7	breast:
6	chr2:47402265..47404474-chr2:47473092..47477391,4	MCF-7	breast:
7	chr2:47400916..47405681-chr2:47469986..47480951,19	K562	blood:
8	chr2:47441944..47444316-chr2:47476312..47479303,2	MCF-7	breast:
9	chr2:47476493..47480049-chr2:47496667..47500826,6	MCF-7	breast:
10	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
11	chr2:47450507..47453723-chr2:47476153..47479003,3	MCF-7	breast:
12	chr2:47465412..47469681-chr2:47474773..47478680,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226087	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10165172	1.00[JPT][hapmap]
rs10165417	1.00[JPT][hapmap]
rs10169583	0.81[EUR][1000 genomes]
rs10191479	0.83[CHD][hapmap]
rs10204202	1.00[JPT][hapmap]
rs12329350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467738	0.83[CHD][hapmap]
rs13383452	0.83[CHD][hapmap]
rs13383554	1.00[JPT][hapmap]
rs13386635	1.00[JPT][hapmap]
rs13412502	1.00[JPT][hapmap]
rs13413278	1.00[JPT][hapmap]
rs13417367	1.00[ASN][1000 genomes]
rs13424419	1.00[JPT][hapmap]
rs17558224	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs55741238	0.80[EUR][1000 genomes]
rs6736764	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749044	1.00[JPT][hapmap]
rs931640	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][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	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	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
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv526478	chr2:47476816-47477584	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12328197	MCFD2	cis	parietal	SCAN
rs12328197	PREPL	cis	cerebellum	SCAN
rs12328197	LOC100129726	cis	parietal	SCAN
rs12328197	RHOQ	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47475800-47477200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:47475800-47477200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:47475800-47478600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:47475800-47478800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:47476000-47477000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:47476000-47477000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:47476000-47477200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:47476000-47477600	Enhancers	Hela-S3	cervix
9	chr2:47476000-47478000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:47476000-47478200	Enhancers	HSMM	muscle
11	chr2:47476000-47479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:47476200-47477000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:47476200-47477200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:47476400-47477000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
15	chr2:47476400-47477000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:47476400-47477200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr2:47476400-47477200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:47476400-47477200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:47476400-47477400	Enhancers	Fetal Intestine Small	intestine
20	chr2:47476400-47478000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:47476400-47478000	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:47476400-47478200	Enhancers	NH-A	brain
23	chr2:47476600-47477000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:47476600-47477000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:47476600-47477000	Active TSS	Stomach Smooth Muscle	stomach
26	chr2:47476600-47477000	Flanking Active TSS	HSMMtube	muscle
27	chr2:47476600-47478000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr2:47476600-47478600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:47476600-47483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:47476800-47477000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:47476800-47477200	Enhancers	Brain Anterior Caudate	brain
32	chr2:47476800-47477800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:47476800-47478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:47476800-47483600	Weak transcription	A549	lung

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