Variant report

Variant	rs12255504
Chromosome Location	chr10:91092189-91092190
allele	C/G
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	POLR2A	chr10:91091907-91094149	GM18505	blood:	n/a	n/a
2	POLR2A	chr10:91091747-91094224	GM19099	blood:	n/a	n/a
3	RELA	chr10:91091894-91093364	GM19193	blood:	n/a	n/a
4	MEF2A	chr10:91091934-91094201	GM12878	blood:	n/a	chr10:91092775-91092786 chr10:91092773-91092789 chr10:91092773-91092788 chr10:91092772-91092793 chr10:91092774-91092788 chr10:91092773-91092790 chr10:91092776-91092787 chr10:91092773-91092788
5	STAT1	chr10:91091869-91092487	K562	blood:	n/a	chr10:91092190-91092201 chr10:91092239-91092250 chr10:91092233-91092244
6	EP300	chr10:91091835-91093070	GM12878	blood:	n/a	chr10:91092457-91092467 chr10:91092235-91092249 chr10:91092192-91092206
7	MTA3	chr10:91091814-91094217	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:91091824-91095564	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:91092036-91093373	GM12892	blood:	n/a	n/a
10	POLR2A	chr10:91091691-91094196	GM18526	blood:	n/a	n/a
11	MYBL2	chr10:91091761-91092519	HepG2	liver:	n/a	n/a
12	PML	chr10:91091814-91094354	GM12878	blood:	n/a	n/a
13	IKZF1	chr10:91091829-91094282	GM12878	blood:	n/a	n/a
14	FOXM1	chr10:91091825-91094360	GM12878	blood:	n/a	n/a
15	CUX1	chr10:91091984-91093259	GM12878	blood:	n/a	chr10:91092813-91092824
16	FOXA1	chr10:91091808-91092595	HepG2	liver:	n/a	chr10:91092454-91092466
17	TBL1XR1	chr10:91092003-91092315	K562	blood:	n/a	n/a
18	BHLHE40	chr10:91091817-91092203	HepG2	liver:	n/a	n/a
19	RELA	chr10:91091923-91094228	GM10847	blood:	n/a	chr10:91094017-91094026 chr10:91094017-91094026 chr10:91093847-91093856 chr10:91093847-91093856
20	MXI1	chr10:91091944-91092194	HepG2	liver:	n/a	n/a
21	MTA3	chr10:91091807-91094338	GM12878	blood:	n/a	n/a
22	RELA	chr10:91091863-91094219	GM15510	blood:	n/a	chr10:91094017-91094026 chr10:91094017-91094026 chr10:91093847-91093856 chr10:91093847-91093856
23	TCF12	chr10:91091871-91092284	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:91092130-91094225	GM12878	blood:	n/a	n/a
25	SPI1	chr10:91092015-91092432	GM12891	blood:	n/a	n/a
26	IRF1	chr10:91091828-91093371	K562	blood:	n/a	chr10:91092187-91092201 chr10:91092189-91092209 chr10:91092233-91092247 chr10:91092228-91092245 chr10:91092231-91092245 chr10:91092233-91092244 chr10:91092232-91092246 chr10:91092238-91092258 chr10:91092238-91092251 chr10:91092190-91092203 chr10:91092234-91092248 chr10:91092190-91092201 chr10:91092185-91092206 chr10:91092232-91092243 chr10:91092233-91092246 chr10:91092190-91092203 chr10:91092232-91092252 chr10:91092228-91092249 chr10:91092234-91092244 chr10:91092191-91092205 chr10:91092189-91092203 chr10:91092233-91092246 chr10:91092236-91092250 chr10:91092183-91092203 chr10:91092412-91092428 chr10:91092191-91092201 chr10:91092233-91092246 chr10:91093190-91093199 chr10:91092190-91092204 chr10:91092233-91092245 chr10:91092230-91092247
27	RELA	chr10:91091771-91094241	GM19099	blood:	n/a	chr10:91094017-91094026 chr10:91094017-91094026 chr10:91093847-91093856 chr10:91093847-91093856
28	POLR2A	chr10:91091883-91094258	GM12892	blood:	n/a	n/a
29	POLR2A	chr10:91091975-91094266	GM12892	blood:	n/a	n/a
30	POLR2A	chr10:91092014-91094283	GM12892	blood:	n/a	n/a
31	POLR2A	chr10:91092001-91094214	GM12892	blood:	n/a	n/a
32	POLR2A	chr10:91091742-91094086	GM19193	blood:	n/a	n/a
33	BHLHE40	chr10:91091306-91094227	GM12878	blood:	n/a	chr10:91092944-91092957
34	POLR2A	chr10:91091906-91094285	GM12878	blood:	n/a	n/a
35	IRF1	chr10:91092034-91092428	K562	blood:	n/a	chr10:91092187-91092201 chr10:91092189-91092209 chr10:91092233-91092247 chr10:91092228-91092245 chr10:91092231-91092245 chr10:91092233-91092244 chr10:91092232-91092246 chr10:91092238-91092258 chr10:91092238-91092251 chr10:91092190-91092203 chr10:91092234-91092248 chr10:91092190-91092201 chr10:91092185-91092206 chr10:91092232-91092243 chr10:91092233-91092246 chr10:91092190-91092203 chr10:91092232-91092252 chr10:91092228-91092249 chr10:91092234-91092244 chr10:91092191-91092205 chr10:91092189-91092203 chr10:91092233-91092246 chr10:91092236-91092250 chr10:91092183-91092203 chr10:91092412-91092428 chr10:91092191-91092201 chr10:91092233-91092246 chr10:91092190-91092204 chr10:91092233-91092245 chr10:91092230-91092247
36	POLR2A	chr10:91092074-91094224	GM12878	blood:	n/a	n/a
37	POLR2A	chr10:91091930-91093280	GM15510	blood:	n/a	n/a
38	SPI1	chr10:91092040-91092347	GM12878	blood:	n/a	n/a
39	POLR2A	chr10:91092112-91094133	GM12878	blood:	n/a	n/a
40	STAT1	chr10:91092094-91092342	GM12878	blood:	n/a	chr10:91092190-91092201 chr10:91092239-91092250 chr10:91092233-91092244
41	CTCF	chr10:91092140-91092290	HBMEC	blood vessel:	n/a	n/a
42	BCLAF1	chr10:91091836-91092731	GM12878	blood:	n/a	chr10:91092192-91092201 chr10:91092235-91092244
43	ATF2	chr10:91091825-91093457	GM12878	blood:	n/a	n/a
44	TAF1	chr10:91092041-91092541	GM12878	blood:	n/a	n/a
45	EBF1	chr10:91091796-91094345	GM12878	blood:	n/a	n/a
46	BHLHE40	chr10:91091877-91092397	K562	blood:	n/a	n/a
47	RELA	chr10:91091925-91093245	GM18526	blood:	n/a	n/a
48	HCFC1	chr10:91092028-91092409	K562	blood:	n/a	n/a
49	TBP	chr10:91092021-91093212	GM12878	blood:	n/a	n/a
50	CHD1	chr10:91091978-91094215	GM12878	blood:	n/a	chr10:91093268-91093278

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91086403..91089519-chr10:91091273..91094339,4	K562	blood:

Variant related genes	Relation type
IFIT3	TF binding region
ENSG00000119917	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10509571	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10509572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788642	0.84[ASN][1000 genomes]
rs10887950	0.90[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10887953	0.95[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs10887957	0.83[ASN][1000 genomes]
rs10887959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap]
rs11203063	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11203066	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11203070	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11203072	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203090	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11203099	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11203105	0.85[ASN][1000 genomes]
rs11203106	0.84[ASN][1000 genomes]
rs11203109	0.95[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs11203115	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs11819073	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12244233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12248331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356008	0.82[ASN][1000 genomes]
rs12766862	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12772449	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12781453	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332330	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1591051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17096301	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17120001	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17120004	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17120325	0.95[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs17121248	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2070845	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2274878	0.86[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34032344	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34234196	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34712773	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35830608	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35833529	0.81[AMR][1000 genomes]
rs3740027	0.81[CEU][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3780878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339948	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4630205	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs59564102	0.87[ASN][1000 genomes]
rs6586182	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6586183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6586196	0.81[CEU][hapmap]
rs7073534	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7085361	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7088579	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7090346	0.90[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7097569	0.81[AMR][1000 genomes]
rs71479013	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7897619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7897873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7910389	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7916812	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884407	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9733018	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12255504	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs12255504	IFIT5	cis	Lymphoblastoid	GTEx
rs12255504	IFIT5	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91087200-91093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91088000-91099800	Weak transcription	Gastric	stomach
3	chr10:91088200-91092400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr10:91088200-91093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:91088200-91093400	Weak transcription	Esophagus	oesophagus
6	chr10:91088400-91092200	Weak transcription	HMEC	breast
7	chr10:91088600-91092200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:91088800-91092200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:91088800-91092200	Enhancers	Left Ventricle	heart
10	chr10:91088800-91092600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:91089000-91092200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:91089000-91092200	Weak transcription	Fetal Heart	heart
13	chr10:91089400-91092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:91090000-91092400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr10:91090200-91107600	Weak transcription	Pancreas	Pancrea
16	chr10:91090400-91092200	Weak transcription	Lung	lung
17	chr10:91090400-91092600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr10:91090400-91092600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:91090600-91092200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:91090600-91092200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:91090600-91092200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:91090600-91092600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:91090800-91092200	Enhancers	Brain Angular Gyrus	brain
24	chr10:91091000-91092200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:91091000-91092200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:91091000-91092400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr10:91091200-91094000	Enhancers	Fetal Brain Male	brain
28	chr10:91091400-91092400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:91091400-91092800	Weak transcription	Spleen	Spleen
30	chr10:91091600-91093400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr10:91091600-91094200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr10:91091800-91092200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:91091800-91092200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr10:91091800-91092200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:91091800-91092200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:91091800-91092200	Active TSS	HSMMtube	muscle
37	chr10:91091800-91092200	Enhancers	K562	blood
38	chr10:91091800-91092200	Flanking Active TSS	NHDF-Ad	bronchial
39	chr10:91091800-91092400	Active TSS	Fetal Intestine Small	intestine
40	chr10:91091800-91092400	Enhancers	Small Intestine	intestine
41	chr10:91091800-91092600	Active TSS	Colon Smooth Muscle	Colon
42	chr10:91091800-91092600	Flanking Active TSS	Dnd41	blood
43	chr10:91091800-91092800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr10:91091800-91092800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr10:91091800-91092800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:91091800-91092800	Flanking Active TSS	Fetal Kidney	kidney
47	chr10:91091800-91092800	Flanking Active TSS	Fetal Lung	lung
48	chr10:91091800-91092800	Active TSS	Rectal Smooth Muscle	rectum
49	chr10:91091800-91092800	Active TSS	GM12878-XiMat	blood
50	chr10:91091800-91093000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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