Variant report

Variant	rs304501
Chromosome Location	chr10:91135132-91135133
allele	C/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	GATA1	chr10:91133912-91135158	K562	blood:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
2	FOXA1	chr10:91135125-91135479	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
IFIT1B	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10788641	0.94[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10887942	0.82[EUR][1000 genomes]
rs10887945	0.84[EUR][1000 genomes]
rs10887946	0.94[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10887947	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs10887948	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11203064	0.82[EUR][1000 genomes]
rs11203065	0.83[EUR][1000 genomes]
rs11203078	0.94[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1141862	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12220939	0.84[EUR][1000 genomes]
rs188589	0.81[JPT][hapmap]
rs191027	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs303210	0.81[JPT][hapmap];0.85[MEX][hapmap]
rs303212	0.86[MEX][hapmap]
rs303215	0.81[JPT][hapmap]
rs303218	0.84[MEX][hapmap]
rs304411	0.85[MEX][hapmap]
rs304437	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs304493	0.89[GIH][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs304502	0.81[JPT][hapmap]
rs304505	0.81[JPT][hapmap];0.85[MEX][hapmap]
rs304506	0.81[JPT][hapmap]
rs304508	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs305374	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4934472	0.82[EUR][1000 genomes]
rs627127	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs627496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs781501	0.89[EUR][1000 genomes]
rs812451	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS 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	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs304501	LIPA	cis	parietal	SCAN
rs304501	IFIT5	cis	cerebellum	SCAN
rs304501	IFIT1	cis	cerebellum	SCAN
rs304501	IFIT5	cis	parietal	SCAN
rs304501	IFIT5	cis	Nerve Tibial	GTEx
rs304501	IFIT5	cis	Artery Tibial	GTEx
rs304501	IFIT5	cis	lymphoblastoid	seeQTL
rs304501	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304501	IFIT5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91129400-91138000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr10:91130600-91135800	Enhancers	Liver	Liver
3	chr10:91130800-91135800	Enhancers	Fetal Heart	heart
4	chr10:91131000-91135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:91131200-91135200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:91133000-91135200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:91133000-91135400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr10:91133000-91135400	Enhancers	Fetal Intestine Small	intestine
9	chr10:91133200-91135200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:91133200-91135200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:91133200-91135200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:91133200-91135200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr10:91133200-91135200	Enhancers	Fetal Muscle Leg	muscle
14	chr10:91133200-91135200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr10:91133200-91135200	Enhancers	NHDF-Ad	bronchial
16	chr10:91133200-91135200	Enhancers	NHLF	lung
17	chr10:91133200-91135400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:91133200-91135400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:91133200-91135600	Enhancers	Fetal Intestine Large	intestine
20	chr10:91133200-91135800	Enhancers	Brain Substantia Nigra	brain
21	chr10:91133400-91135200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr10:91133800-91135200	Enhancers	Aorta	Aorta
23	chr10:91133800-91135800	Enhancers	Pancreas	Pancrea
24	chr10:91134000-91135200	Enhancers	Spleen	Spleen
25	chr10:91134200-91135200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:91134200-91135200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:91134200-91135200	Enhancers	Adipose Nuclei	Adipose
28	chr10:91134200-91135200	Enhancers	Ovary	ovary
29	chr10:91134200-91135200	Enhancers	NH-A	brain
30	chr10:91134200-91135400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:91134200-91138000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr10:91134400-91135200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr10:91134400-91135600	Enhancers	HepG2	liver
34	chr10:91134800-91135200	Enhancers	K562	blood
35	chr10:91134800-91135600	Enhancers	Brain Hippocampus Middle	brain
36	chr10:91134800-91135600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr10:91134800-91135800	Enhancers	Brain Cingulate Gyrus	brain
38	chr10:91134800-91142600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:91135000-91135200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr10:91135000-91135400	Enhancers	Brain Anterior Caudate	brain
41	chr10:91135000-91135600	Enhancers	Brain Angular Gyrus	brain
42	chr10:91135000-91135800	Enhancers	Fetal Lung	lung
43	chr10:91135000-91150200	Weak transcription	Fetal Brain Male	brain

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