Variant report

Variant	rs997456
Chromosome Location	chr10:91403980-91403981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:408)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:408 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr10:91403684-91404223	A549	lung:	n/a	n/a
2	SMC3	chr10:91403946-91404335	K562	blood:	n/a	n/a
3	TAF1	chr10:91403751-91404124	Hela-S3	cervix:	n/a	n/a
4	TAF1	chr10:91403746-91404162	GM12891	blood:	n/a	n/a
5	FOXA1	chr10:91403441-91404062	HepG2	liver:	n/a	n/a
6	BHLHE40	chr10:91403636-91404650	K562	blood:	n/a	n/a
7	POLR2A	chr10:91403700-91405389	A549	lung:	n/a	n/a
8	POLR2A	chr10:91403716-91404203	U87	brain:	n/a	n/a
9	POLR2A	chr10:91403400-91405426	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr10:91403355-91404197	HepG2	liver:	n/a	n/a
11	TAF1	chr10:91403621-91404302	MCF-7	breast:	n/a	n/a
12	SP1	chr10:91403364-91404211	HepG2	liver:	n/a	chr10:91403781-91403802 chr10:91403717-91403738
13	ELF1	chr10:91403579-91404082	GM12878	blood:	n/a	n/a
14	MXI1	chr10:91403283-91406204	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:91403586-91405802	K562	blood:	n/a	n/a
16	TAF1	chr10:91403623-91404187	PFSK-1	brain:	n/a	n/a
17	EP300	chr10:91403554-91404076	H1-hESC	embryonic stem cell:	n/a	chr10:91403972-91403988
18	NFIC	chr10:91403491-91404092	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:91403437-91405448	K562	blood:	n/a	n/a
20	POLR2A	chr10:91403723-91404648	HepG2	liver:	n/a	n/a
21	TBL1XR1	chr10:91403257-91404363	K562	blood:	n/a	n/a
22	WRNIP1	chr10:91403584-91404183	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:91403641-91405454	A549	lung:	n/a	n/a
24	YY1	chr10:91403742-91405560	HepG2	liver:	n/a	chr10:91404302-91404316
25	UBTF	chr10:91403448-91405324	K562	blood:	n/a	n/a
26	POLR2A	chr10:91403597-91405490	GM18951	blood:	n/a	n/a
27	TAF1	chr10:91403545-91404483	MCF-7	breast:	n/a	n/a
28	CREB1	chr10:91403583-91405549	GM12878	blood:	n/a	n/a
29	SETDB1	chr10:91403294-91404094	U2OS	brain:	n/a	n/a
30	REST	chr10:91403731-91404067	SK-N-SH	brain:	n/a	n/a
31	MAX	chr10:91403457-91405754	A549	lung:	n/a	chr10:91405450-91405460
32	POLR2A	chr10:91403303-91404544	HepG2	liver:	n/a	n/a
33	REST	chr10:91403725-91404145	PFSK-1	brain:	n/a	n/a
34	TCF3	chr10:91403798-91404054	GM12878	blood:	n/a	chr10:91404028-91404037
35	POLR2A	chr10:91403689-91405445	GM18526	blood:	n/a	n/a
36	SMARCB1	chr10:91403699-91405465	Hela-S3	cervix:	n/a	n/a
37	USF2	chr10:91403600-91403991	H1-hESC	embryonic stem cell:	n/a	chr10:91403748-91403759
38	POLR2A	chr10:91403587-91405376	HUVEC	blood vessel:	n/a	n/a
39	CHD1	chr10:91403595-91405162	GM12878	blood:	n/a	n/a
40	SP1	chr10:91403414-91404426	HCT-116	colon:	n/a	chr10:91403781-91403802 chr10:91403717-91403738
41	ELK1	chr10:91403496-91403999	GM12878	blood:	n/a	n/a
42	REST	chr10:91403679-91404086	SK-N-SH	brain:	n/a	n/a
43	CEBPD	chr10:91403516-91405139	HepG2	liver:	n/a	chr10:91403624-91403635
44	HDAC2	chr10:91403443-91404000	HepG2	liver:	n/a	n/a
45	BHLHE40	chr10:91403644-91406106	HepG2	liver:	n/a	n/a
46	FOXA2	chr10:91403384-91404134	HepG2	liver:	n/a	n/a
47	STAT1	chr10:91403631-91404112	GM12878	blood:	n/a	n/a
48	POLR2A	chr10:91403417-91404803	HepG2	liver:	n/a	n/a
49	MAX	chr10:91403560-91405896	K562	blood:	n/a	chr10:91405450-91405460
50	POLR2A	chr10:91403380-91405480	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:91403635..91406711-chr10:91457604..91462894,9	MCF-7	breast:
2	chr10:91403655..91404330-chr9:130213244..130214014,2	NB4	blood:
3	chr10:91402369..91405488-chr10:91459565..91463449,8	K562	blood:
4	chr10:91403333..91404068-chr15:65588290..65588813,2	Hela-S3	cervix:
5	chr10:91371070..91374344-chr10:91402272..91406788,6	MCF-7	breast:
6	chr10:91369955..91372663-chr10:91402410..91404170,2	K562	blood:
7	chr10:91401983..91406312-chr10:91459063..91463449,10	K562	blood:
8	chr10:91402267..91405688-chr10:91407429..91411344,10	K562	blood:
9	chr10:70480750..70481482-chr10:91403808..91404438,2	Hela-S3	cervix:
10	chr10:91403809..91404792-chr4:73935189..73935933,2	NB4	blood:
11	chr10:91403860..91404543-chr17:54991495..54992488,2	Hela-S3	cervix:
12	chr10:91402561..91404356-chr12:56108835..56111046,2	MCF-7	breast:
13	chr10:91403856..91404455-chr19:13263583..13264426,2	Hela-S3	cervix:
14	chr10:91403504..91404306-chr7:91874779..91875485,2	NB4	blood:
15	chr10:91403572..91404172-chr19:49588652..49589213,2	Hela-S3	cervix:
16	chr10:91402715..91410625-chr10:91458897..91464646,18	MCF-7	breast:
17	chr10:91403668..91404273-chr3:186500942..186501784,2	Hela-S3	cervix:
18	chr10:91403863..91404498-chr10:124913819..124914546,2	Hela-S3	cervix:
19	chr10:91403856..91404431-chr16:89988692..89989667,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
PANK1	TF binding region
ENSG00000232936	TF binding region
ENSG00000148356	Chromatin interaction
ENSG00000235100	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000104852	Chromatin interaction
ENSG00000060339	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000240996	Chromatin interaction
ENSG00000163626	Chromatin interaction
ENSG00000001631	Chromatin interaction
ENSG00000154473	Chromatin interaction
ENSG00000156976	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000138182	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000225836	Chromatin interaction
ENSG00000135441	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11593819	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593892	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11594682	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598015	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598257	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413697	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414849	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415422	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326195	1.00[ASN][1000 genomes]
rs17484219	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026553	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354493	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426060	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56318555	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071258	1.00[ASN][1000 genomes]
rs72818732	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818736	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818740	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818744	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818750	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818751	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818757	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818758	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818759	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818766	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818768	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818770	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818773	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818774	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818781	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818783	0.84[EUR][1000 genomes]
rs72818786	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818790	1.00[ASN][1000 genomes]
rs72818792	1.00[ASN][1000 genomes]
rs728852	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419628	chr10:91403597-91406145	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs997456	IFIT5	cis	lymphoblastoid	seeQTL
rs997456	GAP43	trans	lymphoblastoid	seeQTL
rs997456	IFIT1	cis	lymphoblastoid	seeQTL
rs997456	SMARCA2	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91401000-91405200	Active TSS	GM12878-XiMat	blood
2	chr10:91401600-91405200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr10:91401600-91405400	Active TSS	Fetal Kidney	kidney
4	chr10:91402000-91405200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr10:91402000-91405200	Active TSS	Liver	Liver
6	chr10:91402000-91405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr10:91402000-91405400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr10:91402000-91405800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:91402200-91405200	Active TSS	Fetal Intestine Small	intestine
10	chr10:91402200-91405400	Active TSS	K562	blood
11	chr10:91402400-91405200	Active TSS	HepG2	liver
12	chr10:91402400-91405400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:91402600-91404200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr10:91402600-91405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:91402600-91405200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr10:91402600-91405400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:91402600-91405400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:91402800-91405200	Active TSS	HMEC	breast
19	chr10:91402800-91405200	Active TSS	NHLF	lung
20	chr10:91402800-91405400	Active TSS	Fetal Muscle Leg	muscle
21	chr10:91403000-91404000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:91403000-91404200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:91403000-91404200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:91403000-91404400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:91403000-91404800	Active TSS	Right Atrium	heart
26	chr10:91403000-91405200	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr10:91403000-91405200	Active TSS	Fetal Intestine Large	intestine
28	chr10:91403000-91405200	Active TSS	Hela-S3	cervix
29	chr10:91403000-91405200	Active TSS	NHDF-Ad	bronchial
30	chr10:91403000-91405400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr10:91403000-91405400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:91403000-91405400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:91403000-91405400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:91403000-91405400	Active TSS	Brain Germinal Matrix	brain
35	chr10:91403000-91405400	Active TSS	Psoas Muscle	Psoas
36	chr10:91403000-91405400	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr10:91403000-91405600	Active TSS	Fetal Muscle Trunk	muscle
38	chr10:91403000-91405800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr10:91403200-91404200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr10:91403200-91404200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr10:91403200-91404200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr10:91403200-91404200	Flanking Active TSS	HUVEC	blood vessel
43	chr10:91403200-91404200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr10:91403200-91404600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:91403200-91405200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr10:91403200-91405200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:91403200-91405200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:91403200-91405200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr10:91403200-91405200	Active TSS	Brain Substantia Nigra	brain
50	chr10:91403200-91405200	Active TSS	Colonic Mucosa	Colon

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