Variant report

Variant	rs17484219
Chromosome Location	chr10:91479211-91479212
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	STAT3	chr10:91479120-91479279	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr10:91479106-91480380	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:91478868..91481810-chr10:91491858..91494458,2	K562	blood:
2	chr10:91460830..91462957-chr10:91478457..91481864,3	MCF-7	breast:
3	chr10:91477849..91480081-chr10:91482106..91484005,3	K562	blood:

Variant related genes	Relation type
KIF20B	TF binding region
ENSG00000138182	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11593819	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593892	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11594682	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595126	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597847	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598015	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598257	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413697	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414269	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414650	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12414849	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415422	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326195	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026553	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354493	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35059516	1.00[ASN][1000 genomes]
rs4426060	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56318555	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071258	1.00[ASN][1000 genomes]
rs72818732	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818736	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818744	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818750	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818751	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818759	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818766	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818768	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818770	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818773	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818774	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818781	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818783	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72818786	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818790	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818792	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728852	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997456	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1054572	chr10:91471956-91537070	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17484219	IFIT5	cis	lymphoblastoid	seeQTL
rs17484219	SMARCA2	trans	lymphoblastoid	seeQTL
rs17484219	GAP43	trans	lymphoblastoid	seeQTL
rs17484219	KIF20B	cis	parietal	SCAN
rs17484219	IFIT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91461600-91546600	Weak transcription	Small Intestine	intestine
2	chr10:91461800-91505800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:91462000-91505800	Weak transcription	Left Ventricle	heart
4	chr10:91462200-91480400	Weak transcription	Fetal Stomach	stomach
5	chr10:91462200-91480600	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:91462200-91482400	Weak transcription	Pancreas	Pancrea
7	chr10:91462200-91486400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr10:91462200-91505600	Weak transcription	Esophagus	oesophagus
9	chr10:91462200-91505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:91462200-91505800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:91462200-91505800	Weak transcription	Gastric	stomach
12	chr10:91462200-91505800	Weak transcription	Lung	lung
13	chr10:91462400-91480000	Weak transcription	Fetal Kidney	kidney
14	chr10:91462400-91480600	Weak transcription	Primary T cells from cord blood	blood
15	chr10:91462400-91480600	Weak transcription	Fetal Intestine Small	intestine
16	chr10:91462400-91484600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:91462400-91488600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:91462400-91505600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:91463400-91480600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:91463400-91484200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:91463400-91505600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:91463400-91505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:91463400-91521600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:91464000-91486800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:91465600-91479400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:91465800-91505600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr10:91466200-91484200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:91466600-91506800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:91467000-91491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:91467200-91489000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:91467200-91489000	Weak transcription	K562	blood
32	chr10:91467200-91505600	Weak transcription	Fetal Brain Female	brain
33	chr10:91467400-91498200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:91467600-91538400	Weak transcription	Fetal Heart	heart
35	chr10:91467800-91507200	Weak transcription	Fetal Brain Male	brain
36	chr10:91468600-91488000	Weak transcription	Aorta	Aorta
37	chr10:91468800-91506600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:91469200-91505000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:91469400-91494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:91469600-91523600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:91470000-91503800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:91470200-91484600	Weak transcription	Ovary	ovary
43	chr10:91470200-91505800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:91470400-91486600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:91470400-91494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr10:91471000-91480600	Weak transcription	NHLF	lung
47	chr10:91472400-91484000	Weak transcription	Thymus	Thymus
48	chr10:91472600-91530200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:91473600-91505600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr10:91473800-91505800	Weak transcription	Liver	Liver

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