Variant report

Variant	rs1699499
Chromosome Location	chr9:98008381-98008382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98003959..98008531-chr9:98008535..98011761,4	K562	blood:
2	chr9:98007562..98009225-chr9:98010300..98012768,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10761371	0.86[EUR][1000 genomes]
rs10993471	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1564235	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1871220	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1888945	0.86[EUR][1000 genomes]
rs1888946	0.86[EUR][1000 genomes]
rs2810914	1.00[AMR][1000 genomes]
rs4743978	0.86[EUR][1000 genomes]
rs600654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479596	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6479597	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7039768	0.86[EUR][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1699499	FBP1	cis	lymphoblastoid	seeQTL
rs1699499	TNIK	trans	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97973600-98024000	Weak transcription	Gastric	stomach
2	chr9:97974000-98009400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:97978000-98008400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:97981400-98012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:97981600-98009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:97983400-98012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:97987200-98015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:97987800-98008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:97988400-98012200	Weak transcription	Fetal Kidney	kidney
10	chr9:97989200-98009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:97989200-98012400	Weak transcription	Ovary	ovary
12	chr9:97989400-98012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97989400-98013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:97989600-98012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97989800-98011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:97990200-98013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:97990400-98012600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:97991000-98010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:97992400-98008800	Weak transcription	Right Ventricle	heart
21	chr9:97992600-98013400	Weak transcription	Liver	Liver
22	chr9:97993000-98008400	Weak transcription	Adipose Nuclei	Adipose
23	chr9:97993200-98008400	Weak transcription	Spleen	Spleen
24	chr9:97993800-98008800	Weak transcription	Lung	lung
25	chr9:97994200-98011400	Weak transcription	Hela-S3	cervix
26	chr9:97994600-98008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:97994800-98011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:97994800-98017200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:97995400-98012800	Weak transcription	HSMM	muscle
30	chr9:97996400-98012400	Weak transcription	Psoas Muscle	Psoas
31	chr9:97996800-98012800	Weak transcription	HSMMtube	muscle
32	chr9:97997400-98009000	Weak transcription	GM12878-XiMat	blood
33	chr9:97997600-98012400	Weak transcription	Fetal Brain Male	brain
34	chr9:97999800-98019000	Weak transcription	Aorta	Aorta
35	chr9:98001200-98012400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:98002200-98008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:98002400-98008800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:98002400-98015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:98002600-98008400	Weak transcription	Fetal Stomach	stomach
40	chr9:98002600-98008400	Weak transcription	Pancreas	Pancrea
41	chr9:98002600-98008400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:98002600-98008800	Weak transcription	Left Ventricle	heart
43	chr9:98002600-98012400	Weak transcription	Esophagus	oesophagus
44	chr9:98004000-98011200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr9:98004800-98008400	Weak transcription	Dnd41	blood
46	chr9:98004800-98012200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:98005200-98012400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:98005400-98012400	Weak transcription	Fetal Thymus	thymus
49	chr9:98005400-98013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:98005600-98012400	Weak transcription	Colon Smooth Muscle	Colon

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