Variant report

Variant	rs9813644
Chromosome Location	chr3:49918751-49918752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49916166-49923391	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49917897-49920397	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:49918314-49920607	HCT-116	colon:	n/a	n/a
4	POLR2A	chr3:49911230-49922975	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:49917041-49920433	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:49918330-49918790	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:49918306-49920583	HCT-116	colon:	n/a	n/a
8	NR2F2	chr3:49918541-49918862	K562	blood:	n/a	n/a
9	POLR2A	chr3:49918433-49918940	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49917501..49919424-chr3:49920193..49922389,2	K562	blood:
2	chr3:49916844..49918945-chr3:49938759..49941090,2	K562	blood:
3	chr3:49908054..49910878-chr3:49916403..49919498,3	K562	blood:
4	chr3:49918459..49920341-chr3:49922556..49924105,2	K562	blood:
5	chr3:49918643..49920553-chr3:49922837..49925319,3	MCF-7	breast:

No data

Variant related genes	Relation type
ACTBP13	TF binding region
ENSG00000164078	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11130223	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130225	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130230	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130237	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130239	0.84[ASW][hapmap];0.86[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11916261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11920034	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923132	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11924670	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925156	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12486470	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12486832	0.96[EUR][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12490944	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12492291	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493565	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12494077	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494172	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494916	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495114	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495831	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629129	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12629677	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12630917	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630959	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631248	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12631309	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12631608	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12632751	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636045	0.87[AMR][1000 genomes]
rs12636669	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12637222	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12637457	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637681	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12638046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023951	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023952	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28478136	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35333166	0.87[AMR][1000 genomes]
rs41291716	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55643042	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57009357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57575459	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58025924	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58621288	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58766761	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59802870	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61263937	0.82[EUR][1000 genomes]
rs61491513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61729114	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62260717	0.88[EUR][1000 genomes]
rs62260756	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262060	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262095	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262096	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262099	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262100	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262104	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262105	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262116	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262117	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262136	0.81[AMR][1000 genomes]
rs62262138	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262144	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262145	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262148	0.96[EUR][1000 genomes]
rs62263578	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62263580	0.88[EUR][1000 genomes]
rs62263584	0.88[EUR][1000 genomes]
rs62263586	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263588	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263590	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263591	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263600	0.87[AMR][1000 genomes]
rs6797500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9813644	MON1A	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49912000-49919000	Weak transcription	Spleen	Spleen
2	chr3:49914200-49918800	Enhancers	Fetal Brain Male	brain
3	chr3:49914600-49920200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:49917000-49920200	Enhancers	Fetal Intestine Small	intestine
5	chr3:49917200-49918800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:49917200-49919000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:49917200-49919400	Enhancers	Fetal Lung	lung
8	chr3:49917200-49919400	Enhancers	Stomach Smooth Muscle	stomach
9	chr3:49917200-49919400	Enhancers	K562	blood
10	chr3:49917200-49919600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:49917200-49920000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49917200-49920200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:49917200-49920200	Enhancers	Fetal Intestine Large	intestine
14	chr3:49917200-49920400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:49917400-49919200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:49917800-49918800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:49917800-49918800	Enhancers	Brain Germinal Matrix	brain
18	chr3:49917800-49919600	Enhancers	Stomach Mucosa	stomach
19	chr3:49917800-49920200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:49917800-49920200	Enhancers	Right Ventricle	heart
21	chr3:49917800-49920200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:49917800-49920400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:49918000-49918800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:49918000-49918800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr3:49918000-49919000	Flanking Active TSS	Fetal Brain Female	brain
26	chr3:49918000-49919000	Enhancers	Gastric	stomach
27	chr3:49918000-49919600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr3:49918000-49919800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:49918000-49919800	Enhancers	Brain Angular Gyrus	brain
30	chr3:49918000-49920000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr3:49918000-49920000	Enhancers	Brain Anterior Caudate	brain
32	chr3:49918000-49920200	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr3:49918000-49920200	Enhancers	Fetal Stomach	stomach
34	chr3:49918000-49920200	Enhancers	Psoas Muscle	Psoas
35	chr3:49918000-49920200	Enhancers	Right Atrium	heart
36	chr3:49918000-49920400	Enhancers	Left Ventricle	heart
37	chr3:49918200-49918800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:49918200-49919600	Enhancers	Fetal Heart	heart
39	chr3:49918200-49920400	Enhancers	Placenta	Placenta
40	chr3:49918400-49918800	Weak transcription	Hela-S3	cervix
41	chr3:49918400-49919400	Enhancers	Esophagus	oesophagus
42	chr3:49918400-49919600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:49918400-49919600	Enhancers	Fetal Thymus	thymus
44	chr3:49918400-49919800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:49918400-49919800	Weak transcription	Brain Substantia Nigra	brain
46	chr3:49918400-49920000	Enhancers	H9 Cell Line	embryonic stem cell
47	chr3:49918400-49920000	Enhancers	Ovary	ovary
48	chr3:49918400-49920200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:49918600-49918800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:49918600-49918800	Enhancers	Colonic Mucosa	Colon

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