Variant report

Variant	rs2285830
Chromosome Location	chr12:48125764-48125765
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48098253..48100778-chr12:48124904..48127271,2	MCF-7	breast:
2	chr12:48123429..48125813-chr12:48228513..48231351,2	MCF-7	breast:
3	chr12:48125574..48127133-chr12:48129980..48132497,2	MCF-7	breast:
4	chr12:48117242..48121350-chr12:48124704..48128284,5	MCF-7	breast:
5	chr12:48125664..48127471-chr12:48127761..48129880,2	MCF-7	breast:
6	chr12:48124296..48127190-chr12:48166396..48170138,3	MCF-7	breast:
7	chr12:48125681..48127721-chr12:48144377..48147323,2	K562	blood:
8	chr12:48118637..48121187-chr12:48125569..48128782,4	K562	blood:
9	chr12:48122622..48126569-chr12:48133427..48136331,4	K562	blood:
10	chr12:48123494..48126163-chr12:48177951..48180667,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000268069	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10875683	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs11168194	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs11168211	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168212	0.99[ASN][1000 genomes]
rs11168219	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168220	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11830795	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11834770	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1235152	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12812460	0.83[ASN][1000 genomes]
rs12812960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12819759	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12820269	0.81[ASN][1000 genomes]
rs12828238	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003471	0.89[ASN][1000 genomes]
rs2074531	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2074532	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2074534	0.81[LWK][hapmap]
rs2238144	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2239188	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2283345	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3764015	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3764016	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764018	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3764019	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3764020	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4505143	0.94[ASN][1000 genomes]
rs4537844	0.81[ASN][1000 genomes]
rs6580635	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6580636	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7133585	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs726588	0.94[ASN][1000 genomes]
rs7302276	0.83[ASN][1000 genomes]
rs7306556	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs757284	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs7967336	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7967546	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7976708	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
6	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2285830	RAPGEF3	cis	parietal	SCAN
rs2285830	TMEM117	cis	cerebellum	SCAN
rs2285830	PUS7L	cis	parietal	SCAN
rs2285830	RAPGEF3	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:48112600-48128600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:48114600-48128800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:48115200-48126200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
11	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:48116800-48130200	Weak transcription	Aorta	Aorta
13	chr12:48117000-48129000	Weak transcription	Psoas Muscle	Psoas
14	chr12:48118200-48128800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:48119000-48126000	Enhancers	NHDF-Ad	bronchial
16	chr12:48119800-48128600	Weak transcription	Colonic Mucosa	Colon
17	chr12:48120400-48128600	Weak transcription	NH-A	brain
18	chr12:48121400-48125800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:48122800-48126400	Enhancers	Fetal Heart	heart
20	chr12:48123000-48125800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:48123000-48128400	Weak transcription	Spleen	Spleen
22	chr12:48123600-48127000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:48123600-48128600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:48123600-48128600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:48123800-48128200	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:48124000-48127400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:48124200-48126800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:48124200-48127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:48124200-48128400	Weak transcription	Fetal Kidney	kidney
30	chr12:48124200-48130000	Weak transcription	Liver	Liver
31	chr12:48124400-48126400	Weak transcription	Right Atrium	heart
32	chr12:48124400-48129000	Weak transcription	Gastric	stomach
33	chr12:48124400-48129600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:48124600-48125800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:48124600-48126800	Weak transcription	Esophagus	oesophagus
36	chr12:48124600-48128200	Weak transcription	HSMMtube	muscle
37	chr12:48124600-48128400	Weak transcription	Lung	lung
38	chr12:48124600-48128600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:48124600-48130000	Weak transcription	K562	blood
40	chr12:48124800-48125800	Weak transcription	Adipose Nuclei	Adipose
41	chr12:48124800-48125800	Weak transcription	Brain Anterior Caudate	brain
42	chr12:48124800-48126800	Weak transcription	Ovary	ovary
43	chr12:48124800-48126800	Weak transcription	Right Ventricle	heart
44	chr12:48124800-48128200	Weak transcription	Fetal Lung	lung
45	chr12:48124800-48128800	Weak transcription	HSMM	muscle
46	chr12:48124800-48129400	Weak transcription	NHLF	lung
47	chr12:48124800-48130000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:48125000-48128600	Weak transcription	Pancreas	Pancrea
49	chr12:48125400-48126000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:48125400-48126000	Enhancers	Muscle Satellite Cultured Cells	--

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