Variant report

Variant	rs1217375
Chromosome Location	chr1:114346904-114346905
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114299841..114303516-chr1:114345652..114349998,8	MCF-7	breast:
2	chr1:114332999..114335682-chr1:114345986..114348976,2	K562	blood:
3	chr1:114337375..114338962-chr1:114346569..114348868,2	K562	blood:
4	chr1:114346143..114348134-chr1:114470701..114473492,2	K562	blood:
5	chr1:114335674..114337289-chr1:114344913..114347646,2	MCF-7	breast:
6	chr1:114306094..114308491-chr1:114345999..114348043,2	K562	blood:
7	chr1:114336082..114338962-chr1:114345301..114348868,4	K562	blood:
8	chr1:114339066..114343299-chr1:114345760..114348770,4	K562	blood:
9	chr1:114323280..114325938-chr1:114345908..114348853,2	MCF-7	breast:
10	chr1:114300208..114303204-chr1:114345927..114349576,6	K562	blood:
11	chr1:114343967..114345623-chr1:114345810..114347629,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235527	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10858015	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11102678	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1146183	0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs1146184	0.85[CHB][hapmap]
rs1146185	0.81[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap]
rs12144309	0.86[GIH][hapmap]
rs1217378	0.88[AFR][1000 genomes]
rs1217379	0.93[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.90[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs1217403	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1217405	0.86[AFR][1000 genomes]
rs1217406	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1217408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1217411	0.82[AFR][1000 genomes]
rs1217414	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1217417	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217418	0.81[ASW][hapmap];0.97[LWK][hapmap];0.86[YRI][hapmap]
rs1217419	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1230673	0.87[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs1230681	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1230684	0.98[ASN][1000 genomes]
rs1310182	0.88[AFR][1000 genomes]
rs13524	0.93[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs1539437	0.80[AFR][1000 genomes]
rs1624335	0.94[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs1743594	0.94[ASW][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs1746857	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs1935836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1970559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2040041	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185827	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2476599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476600	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs2476602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2476604	0.89[AFR][1000 genomes]
rs2636000	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636003	0.87[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs2797416	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs3789597	1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs3789598	0.91[YRI][hapmap]
rs3789600	0.87[ASW][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4991898	0.85[AFR][1000 genomes]
rs6537798	0.87[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs7555634	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs971173	0.90[JPT][hapmap];0.82[MEX][hapmap]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1217375	MAGI3	cis	cerebellum	SCAN
rs1217375	AP4B1	cis	cerebellum	SCAN
rs1217375	FAM40A	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:114327400-114348800	Weak transcription	Spleen	Spleen
6	chr1:114327400-114351200	Weak transcription	Fetal Brain Male	brain
7	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:114332400-114347200	Weak transcription	Right Atrium	heart
9	chr1:114332400-114353400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:114336000-114351200	Weak transcription	Fetal Brain Female	brain
11	chr1:114336200-114351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:114336200-114351200	Weak transcription	HMEC	breast
13	chr1:114336400-114347000	Weak transcription	NHLF	lung
14	chr1:114336600-114347000	Weak transcription	NHEK	skin
15	chr1:114336600-114347200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:114336600-114347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:114336800-114348400	Weak transcription	Fetal Stomach	stomach
18	chr1:114336800-114349400	Weak transcription	Lung	lung
19	chr1:114337200-114352600	Weak transcription	Fetal Kidney	kidney
20	chr1:114337600-114347000	Weak transcription	Osteobl	bone
21	chr1:114338000-114347000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:114338600-114347000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:114340000-114351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:114340400-114347000	Weak transcription	HSMM	muscle
25	chr1:114340400-114347000	Weak transcription	NHDF-Ad	bronchial
26	chr1:114340400-114352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:114340600-114347000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:114340600-114347000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:114340600-114347000	Weak transcription	Adipose Nuclei	Adipose
30	chr1:114340600-114347000	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:114340600-114347000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:114340600-114347000	Weak transcription	Fetal Lung	lung
33	chr1:114340600-114347000	Weak transcription	NH-A	brain
34	chr1:114340600-114347200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:114340600-114347400	Weak transcription	Primary B cells from cord blood	blood
36	chr1:114340600-114347600	Weak transcription	Fetal Thymus	thymus
37	chr1:114340600-114348000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:114340600-114348400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:114340600-114349400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:114340600-114351400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:114340600-114351400	Weak transcription	Aorta	Aorta
42	chr1:114340600-114351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:114340600-114351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:114340600-114351800	Weak transcription	Thymus	Thymus
45	chr1:114340600-114353400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:114340800-114347000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:114340800-114347000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:114340800-114348000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:114340800-114349400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:114340800-114352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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