Variant report

Variant	rs184236
Chromosome Location	chr10:91179295-91179296
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	RAD21	chr10:91179259-91179647	H1-hESC	embryonic stem cell:	n/a	n/a
2	EBF1	chr10:91179283-91179686	GM12878	blood:	n/a	chr10:91179526-91179537
3	POLR2A	chr10:91179244-91179402	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr10:91179285-91179701	GM12878	blood:	n/a	n/a
5	EBF1	chr10:91179259-91179747	GM12878	blood:	n/a	chr10:91179526-91179537
6	EBF1	chr10:91179274-91179646	GM12878	blood:	n/a	chr10:91179526-91179537
7	RAD21	chr10:91179289-91179589	H1-hESC	embryonic stem cell:	n/a	n/a
8	IRF1	chr10:91179275-91179665	K562	blood:	n/a	n/a
9	CTCF	chr10:91179282-91179672	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91179113..91181163-chr10:91223513..91225946,2	MCF-7	breast:

Variant related genes	Relation type
LIPA	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs188589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188591	0.89[EUR][1000 genomes]
rs2484046	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2484047	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303171	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs303173	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303209	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303210	0.83[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303213	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303215	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303216	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303218	0.97[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs304410	0.80[CEU][hapmap]
rs304411	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304412	0.81[EUR][1000 genomes]
rs304413	0.81[EUR][1000 genomes]
rs304434	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304436	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs304437	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304441	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304442	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304450	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304492	0.89[EUR][1000 genomes]
rs304493	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs304500	0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs304502	0.83[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs304503	0.89[EUR][1000 genomes]
rs304505	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs304506	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs184236	IFIT5	cis	Esophagus Mucosa	GTEx
rs184236	IFIT5	cis	Esophagus Muscularis	GTEx
rs184236	IDE	cis	parietal	SCAN
rs184236	IFIT5	cis	parietal	SCAN
rs184236	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs184236	IFIT1	cis	cerebellum	SCAN
rs184236	IFIT5	cis	lymphoblastoid	seeQTL
rs184236	IFIT5	cis	Artery Tibial	GTEx
rs184236	IFIT1	Cis_1M	lymphoblastoid	RTeQTL
rs184236	LIPA	cis	parietal	SCAN
rs184236	IFIT5	cis	cerebellum	SCAN
rs184236	IFIT5	cis	Thyroid	GTEx
rs184236	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91175400-91180200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91175400-91187600	Weak transcription	HUVEC	blood vessel
3	chr10:91175600-91179600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr10:91175600-91181200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr10:91175600-91181200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:91175600-91183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
9	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
10	chr10:91175800-91179600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:91175800-91182600	Weak transcription	Thymus	Thymus
12	chr10:91176000-91179600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:91176000-91180000	Weak transcription	Colonic Mucosa	Colon
14	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:91176600-91179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:91176600-91182800	Weak transcription	Esophagus	oesophagus
17	chr10:91177000-91181400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:91177200-91181600	Strong transcription	Fetal Intestine Large	intestine
19	chr10:91177200-91181800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr10:91177400-91179800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr10:91177400-91182000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:91177600-91184000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:91177800-91179400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr10:91178000-91179400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr10:91178000-91179400	Enhancers	Brain Substantia Nigra	brain
26	chr10:91178000-91183600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:91178000-91186000	Weak transcription	HMEC	breast
28	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
29	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
30	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:91178200-91179400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr10:91178200-91179400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:91178200-91179600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:91178200-91179600	Enhancers	Brain Cingulate Gyrus	brain
35	chr10:91178200-91179800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:91178200-91180200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:91178200-91180200	Weak transcription	Placenta	Placenta
38	chr10:91178200-91180200	Weak transcription	NHEK	skin
39	chr10:91178200-91180600	Weak transcription	Fetal Heart	heart
40	chr10:91178200-91182200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:91178200-91183800	Weak transcription	HepG2	liver
42	chr10:91178200-91184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
45	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
46	chr10:91178400-91179400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr10:91178400-91179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:91178400-91179400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr10:91178400-91179600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr10:91178400-91179600	Enhancers	Primary B cells from cord blood	blood

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