Variant report

Variant	rs2040041
Chromosome Location	chr1:114312623-114312624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:114312538-114312661	K562	blood:	n/a	n/a
2	GATA3	chr1:114312545-114313105	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114300225..114306650-chr1:114312596..114317597,9	K562	blood:
2	chr1:114301057..114304105-chr1:114310097..114314111,4	MCF-7	breast:
3	chr1:114311260..114313191-chr1:114320305..114322198,2	K562	blood:
4	chr1:114311052..114314058-chr1:114447909..114449535,3	MCF-7	breast:
5	chr1:114310854..114312625-chr1:114314961..114316732,2	MCF-7	breast:
6	chr1:114307794..114309970-chr1:114311148..114314125,2	MCF-7	breast:
7	chr1:114311133..114313597-chr1:114354169..114355783,2	MCF-7	breast:

No data

Variant related genes	Relation type
RSBN1	TF binding region
ENSG00000116793	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10858015	0.85[ASN][1000 genomes]
rs11102678	0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs1146183	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs1146185	1.00[CHD][hapmap];0.94[GIH][hapmap]
rs12144309	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs1217375	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]
rs1217379	0.86[LWK][hapmap]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.90[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1217406	0.91[LWK][hapmap]
rs1217408	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1217414	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs1217417	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217418	0.91[LWK][hapmap]
rs1217419	0.91[LWK][hapmap]
rs1230673	1.00[CHD][hapmap];0.94[GIH][hapmap]
rs1230681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1230684	0.95[ASN][1000 genomes]
rs1235000	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs13524	1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap]
rs1624335	1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap]
rs1743594	0.85[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap]
rs1746857	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1970559	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2185827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2476599	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476600	0.86[LWK][hapmap]
rs2476602	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];0.96[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636000	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636003	1.00[CHD][hapmap];0.94[GIH][hapmap]
rs2797416	0.86[LWK][hapmap]
rs3789597	0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs3789600	0.88[LWK][hapmap]
rs7555634	0.86[LWK][hapmap]
rs971173	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2040041	BCL2L15	cis	cerebellum	SCAN
rs2040041	RAP1A	cis	parietal	SCAN
rs2040041	MAGI3	cis	cerebellum	SCAN
rs2040041	AP4B1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302600-114318000	Weak transcription	Spleen	Spleen
2	chr1:114302600-114321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:114302800-114315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:114302800-114323200	Weak transcription	Aorta	Aorta
5	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
6	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
8	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
9	chr1:114303000-114315800	Weak transcription	Fetal Stomach	stomach
10	chr1:114303000-114318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:114303000-114319000	Weak transcription	Fetal Brain Male	brain
12	chr1:114303000-114319000	Weak transcription	HSMMtube	muscle
13	chr1:114303000-114323200	Weak transcription	Fetal Heart	heart
14	chr1:114303000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:114303200-114317200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:114303200-114328400	Weak transcription	A549	lung
17	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:114304800-114320600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:114307200-114314000	Strong transcription	Primary B cells from cord blood	blood
20	chr1:114307400-114313000	Strong transcription	K562	blood
21	chr1:114308000-114313000	Strong transcription	Fetal Thymus	thymus
22	chr1:114308200-114326600	Weak transcription	Colonic Mucosa	Colon
23	chr1:114309000-114315800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:114309000-114323600	Weak transcription	Gastric	stomach
25	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:114310000-114314400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:114310200-114319000	Weak transcription	Left Ventricle	heart
28	chr1:114310400-114313400	Enhancers	Brain Germinal Matrix	brain
29	chr1:114310400-114313600	Enhancers	Colon Smooth Muscle	Colon
30	chr1:114310600-114317200	Weak transcription	Fetal Brain Female	brain
31	chr1:114310600-114325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:114310800-114315400	Weak transcription	Fetal Lung	lung
33	chr1:114310800-114315600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:114310800-114318600	Weak transcription	HSMM	muscle
35	chr1:114310800-114319400	Weak transcription	NH-A	brain
36	chr1:114310800-114326000	Weak transcription	HMEC	breast
37	chr1:114311000-114314200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:114311000-114315200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:114311000-114315800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:114311000-114315800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:114311000-114316000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:114311000-114316000	Weak transcription	Fetal Intestine Large	intestine
43	chr1:114311000-114316200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:114311000-114316600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:114311000-114316600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:114311000-114316600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:114311000-114316600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:114311000-114316600	Weak transcription	Thymus	Thymus
49	chr1:114311000-114318400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:114311000-114318600	Weak transcription	Hela-S3	cervix

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