Variant report

Variant	rs1384062
Chromosome Location	chr3:99597928-99597929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr3:99597910-99598706	GM12878	blood:	n/a	chr3:99598320-99598333 chr3:99598322-99598331 chr3:99598321-99598334

No.	Distal block	Cell Line	Cell type
1	chr3:99596926..99599142-chr3:99610230..99612159,2	K562	blood:
2	chr3:99542264..99544347-chr3:99597790..99600681,3	K562	blood:
3	chr3:99595513..99598055-chr3:99616729..99618510,2	K562	blood:
4	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
5	chr3:99596775..99598445-chr3:99803201..99805503,2	K562	blood:
6	chr3:99595540..99598482-chr3:99638199..99641058,2	MCF-7	breast:
7	chr3:99535566..99538083-chr3:99597488..99599046,2	K562	blood:

Variant related genes	Relation type
FILIP1L	TF binding region
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1287284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1610509	0.88[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2638948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35422475	0.82[AMR][1000 genomes]
rs4577503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4928230	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4928235	0.81[AMR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs58704213	0.81[ASN][1000 genomes]
rs6440967	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs6802817	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6806323	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs7650727	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs766778	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793440	0.82[TSI][hapmap]
rs793443	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793476	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793503	0.82[TSI][hapmap]
rs796976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs902159	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs923472	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1384062	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs1384062	OR5H6	cis	cerebellum	SCAN
rs1384062	EPHX1	trans	cerebellum	SCAN
rs1384062	SENP7	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595200-99602800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:99595400-99599800	Weak transcription	Pancreas	Pancrea
3	chr3:99595400-99599800	Weak transcription	Spleen	Spleen
4	chr3:99595400-99600000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:99595400-99600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:99595400-99602800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:99595400-99603000	Weak transcription	Stomach Mucosa	stomach
8	chr3:99595400-99603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:99595400-99603400	Weak transcription	Small Intestine	intestine
10	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:99595600-99598800	Weak transcription	Fetal Stomach	stomach
12	chr3:99595600-99599200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:99595600-99599800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:99595600-99599800	Weak transcription	Psoas Muscle	Psoas
15	chr3:99595600-99600400	Weak transcription	Left Ventricle	heart
16	chr3:99595600-99602600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:99595600-99603200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:99595800-99599800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:99595800-99599800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:99595800-99599800	Weak transcription	Right Atrium	heart
23	chr3:99595800-99600400	Weak transcription	Ovary	ovary
24	chr3:99595800-99601200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:99595800-99603200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:99596000-99599600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:99596000-99599800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:99596000-99599800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:99596000-99603000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:99596000-99603200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:99596200-99599600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:99596200-99599600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:99596400-99599800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:99596600-99600200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:99596800-99600400	Weak transcription	Aorta	Aorta
37	chr3:99596800-99601000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:99596800-99602600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:99597000-99599800	Weak transcription	HSMM	muscle
40	chr3:99597000-99603400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:99597200-99602800	Weak transcription	K562	blood
42	chr3:99597200-99603000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:99597200-99603400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:99597200-99614200	Weak transcription	HMEC	breast
45	chr3:99597400-99598600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:99597400-99599600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:99597400-99599600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:99597400-99599800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:99597400-99599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:99597400-99602800	Weak transcription	NHEK	skin

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