Variant report

Variant	rs10040749
Chromosome Location	chr5:111506069-111506070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:122)
Chromatin interactive
region (count:4)
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	chr5:111496280-111506960	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:111505736-111506830	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:111506035-111506085	AG04450	lung:	fetal
2	chr5:111506044-111506094	PFSK-1	brain:	n/a
3	chr5:111506044-111506094	IMR90	lung:	fetal
4	chr5:111506035-111506085	PFSK-1	brain:	n/a
5	chr5:111506035-111506085	HPAEpiC	pulmonary alveolar:	n/a
6	chr5:111506044-111506094	HepG2	liver:	n/a
7	chr5:111506044-111506094	HAEpiC	amniotic membrane:	n/a
8	chr5:111506035-111506085	SK-N-SH	brain:	n/a
9	chr5:111506044-111506094	HMEC	breast:	n/a
10	chr5:111506035-111506085	Jurkat	blood:	n/a
11	chr5:111506044-111506094	K562	blood:	n/a
12	chr5:111506044-111506094	HRE	kidney:	n/a
13	chr5:111506044-111506094	HPAEpiC	pulmonary alveolar:	n/a
14	chr5:111506035-111506085	AG04449	skin:	fetal
15	chr5:111506035-111506085	ovcar-3	ovarian:	n/a
16	chr5:111506035-111506085	AG10803	skin:	n/a
17	chr5:111506044-111506094	NB4	blood:	n/a
18	chr5:111506044-111506094	HCT-116	colon:	n/a
19	chr5:111506035-111506085	Hela-S3	cervix:	n/a
20	chr5:111506044-111506094	SK-N-SH_RA	brain:	n/a
21	chr5:111506044-111506094	CMK	blood:	n/a
22	chr5:111506035-111506085	LNCaP	prostate:	n/a
23	chr5:111506044-111506094	GM12892	blood:	n/a
24	chr5:111506035-111506085	Hepatocyte	liver:	n/a
25	chr5:111506035-111506085	GM06990	blood:	n/a
26	chr5:111506035-111506085	PrEC	prostate:	n/a
27	chr5:111506044-111506094	GM19239	blood:	n/a
28	chr5:111506035-111506085	HCM	heart:	n/a
29	chr5:111506044-111506094	AG09309	skin:	n/a
30	chr5:111506044-111506094	Hepatocyte	liver:	n/a
31	chr5:111506035-111506085	GM19239	blood:	n/a
32	chr5:111506035-111506085	HIPEpiC	eye:	n/a
33	chr5:111506035-111506085	HEK293	kidney:	embryo
34	chr5:111506044-111506094	AG09319	gingival:	n/a
35	chr5:111506035-111506085	MCF10A-Er-Src	breast:	n/a
36	chr5:111506044-111506094	SK-N-MC	brain:	n/a
37	chr5:111506044-111506094	HIPEpiC	eye:	n/a
38	chr5:111506044-111506094	BJ	skin:	n/a
39	chr5:111506035-111506085	HAEpiC	amniotic membrane:	n/a
40	chr5:111506035-111506085	PANC-1	pancreas:	n/a
41	chr5:111506035-111506085	A549	lung:	n/a
42	chr5:111506035-111506085	HRE	kidney:	n/a
43	chr5:111506035-111506085	NHDF-neo	bronchial:	n/a
44	chr5:111506044-111506094	HEK293	kidney:	embryo
45	chr5:111506035-111506085	GM12891	blood:	n/a
46	chr5:111506035-111506085	HRPEpiC	eye:	n/a
47	chr5:111506044-111506094	HRCEpiC	kidney:	n/a
48	chr5:111506035-111506085	GM12892	blood:	n/a
49	chr5:111506035-111506085	ECC-1	luminal epithelium:	n/a
50	chr5:111506035-111506085	AoSMC	blood vessel:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:111504802..111506899-chr5:111509148..111511328,2	MCF-7	breast:
2	chr5:111503980..111506560-chr5:111518097..111522166,4	K562	blood:
3	chr5:111504901..111509125-chr5:111533307..111535722,3	K562	blood:
4	chr5:111505441..111507205-chr5:111752251..111753989,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000250882	TF binding region
ENSG00000250882	CpG island
ENSG00000129595	Chromatin interaction
ENSG00000250882	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10037824	1.00[ASN][1000 genomes]
rs10054560	1.00[ASN][1000 genomes]
rs10054719	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10065740	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10068493	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10069011	1.00[ASN][1000 genomes]
rs10070995	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1020951	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463433	1.00[ASN][1000 genomes]
rs10477478	1.00[ASN][1000 genomes]
rs10478073	1.00[ASN][1000 genomes]
rs1054724	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078128	1.00[ASN][1000 genomes]
rs11241153	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12186685	1.00[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12187589	1.00[ASN][1000 genomes]
rs12188700	1.00[ASN][1000 genomes]
rs12189034	1.00[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13153601	1.00[ASN][1000 genomes]
rs1366144	1.00[ASN][1000 genomes]
rs1427978	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1560052	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560053	1.00[ASN][1000 genomes]
rs1560054	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[ASN][1000 genomes]
rs1560055	1.00[ASN][1000 genomes]
rs1560057	1.00[ASN][1000 genomes]
rs1560058	1.00[ASN][1000 genomes]
rs1560061	1.00[CHD][hapmap]
rs17134319	1.00[ASN][1000 genomes]
rs17134348	1.00[ASN][1000 genomes]
rs17271934	1.00[CHD][hapmap]
rs1896620	1.00[ASN][1000 genomes]
rs1896621	1.00[ASN][1000 genomes]
rs1975015	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114991	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416277	1.00[ASN][1000 genomes]
rs27413	1.00[ASN][1000 genomes]
rs4602685	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4957632	1.00[ASN][1000 genomes]
rs4957634	1.00[ASN][1000 genomes]
rs4957636	1.00[ASN][1000 genomes]
rs4958002	1.00[ASN][1000 genomes]
rs4958003	1.00[ASN][1000 genomes]
rs4958004	1.00[ASN][1000 genomes]
rs4958009	1.00[ASN][1000 genomes]
rs4958010	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4958012	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4958013	1.00[ASN][1000 genomes]
rs4958014	1.00[ASN][1000 genomes]
rs4958015	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4958020	1.00[ASN][1000 genomes]
rs4958025	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs55639430	1.00[ASN][1000 genomes]
rs55796748	1.00[ASN][1000 genomes]
rs55829200	1.00[ASN][1000 genomes]
rs55913426	1.00[ASN][1000 genomes]
rs56108405	1.00[ASN][1000 genomes]
rs56288086	1.00[ASN][1000 genomes]
rs56293447	1.00[ASN][1000 genomes]
rs56307310	1.00[ASN][1000 genomes]
rs56881711	1.00[ASN][1000 genomes]
rs57428532	1.00[ASN][1000 genomes]
rs59537089	1.00[ASN][1000 genomes]
rs60636568	1.00[ASN][1000 genomes]
rs61061658	1.00[ASN][1000 genomes]
rs62367266	1.00[ASN][1000 genomes]
rs62372421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594566	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594567	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594569	1.00[ASN][1000 genomes]
rs6594571	1.00[ASN][1000 genomes]
rs6594574	1.00[ASN][1000 genomes]
rs6594577	1.00[ASN][1000 genomes]
rs6594588	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs66892745	1.00[ASN][1000 genomes]
rs67033649	1.00[ASN][1000 genomes]
rs67586008	1.00[ASN][1000 genomes]
rs67631852	1.00[ASN][1000 genomes]
rs6863063	1.00[ASN][1000 genomes]
rs6872947	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876893	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6878423	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6884589	1.00[ASN][1000 genomes]
rs6893877	1.00[CHD][hapmap]
rs6894036	1.00[CHD][hapmap]
rs72781655	1.00[ASN][1000 genomes]
rs72781664	1.00[ASN][1000 genomes]
rs72781668	1.00[ASN][1000 genomes]
rs72781677	1.00[ASN][1000 genomes]
rs72781678	1.00[ASN][1000 genomes]
rs7703522	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704087	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7706160	1.00[ASN][1000 genomes]
rs7709484	1.00[ASN][1000 genomes]
rs7710973	1.00[ASN][1000 genomes]
rs7711158	1.00[ASN][1000 genomes]
rs7716309	1.00[ASN][1000 genomes]
rs7717160	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717363	1.00[ASN][1000 genomes]
rs7719346	1.00[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7722291	1.00[ASN][1000 genomes]
rs821736	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs821749	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs890757	1.00[ASN][1000 genomes]
rs890758	1.00[ASN][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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10040749	STARD4	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111497600-111538600	Weak transcription	Small Intestine	intestine
2	chr5:111498200-111518800	Weak transcription	Right Atrium	heart
3	chr5:111498400-111506400	Strong transcription	Fetal Kidney	kidney
4	chr5:111498400-111506800	Strong transcription	Adipose Nuclei	Adipose
5	chr5:111498600-111506600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:111498800-111506800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:111498800-111507600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:111499600-111507200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:111499600-111510800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:111499800-111510600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:111500000-111510600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:111500200-111510600	Weak transcription	Brain Anterior Caudate	brain
13	chr5:111500400-111510600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:111500600-111508800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:111500800-111510600	Weak transcription	NHEK	skin
16	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
17	chr5:111502200-111510600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:111502200-111510600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:111502200-111510600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:111502200-111511000	Weak transcription	Brain Substantia Nigra	brain
21	chr5:111502400-111510600	Weak transcription	Fetal Heart	heart
22	chr5:111502400-111510600	Weak transcription	K562	blood
23	chr5:111502400-111510600	Weak transcription	NH-A	brain
24	chr5:111502400-111518800	Weak transcription	Pancreas	Pancrea
25	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
26	chr5:111502600-111506200	Weak transcription	NHLF	lung
27	chr5:111502600-111506600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:111502600-111507000	Weak transcription	HMEC	breast
29	chr5:111502600-111509600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:111502600-111510600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:111502600-111510600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:111502600-111510600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:111502600-111510600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:111502600-111510600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:111502600-111510600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:111502800-111507200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:111502800-111509800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:111502800-111510600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:111502800-111546000	Weak transcription	Ovary	ovary
40	chr5:111503000-111510400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:111503000-111510600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:111503400-111508600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:111503600-111506800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr5:111503600-111507000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:111503600-111510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:111503600-111510600	Weak transcription	Brain Angular Gyrus	brain
47	chr5:111503600-111510600	Weak transcription	Fetal Intestine Small	intestine
48	chr5:111503600-111510600	Weak transcription	Dnd41	blood
49	chr5:111503600-111519000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:111503600-111527800	Weak transcription	Psoas Muscle	Psoas

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