Variant report

Variant	rs578327
Chromosome Location	chr9:27193847-27193848
allele	C/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	FOSL1	chr9:27193803-27195107	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
2	CBX3	chr9:27193803-27195211	HCT-116	colon:	n/a	n/a
3	FOSL1	chr9:27193842-27195029	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
4	JUND	chr9:27193763-27194959	SK-N-SH	brain:	n/a	chr9:27194083-27194094 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626

Variant related genes	Relation type
RNA5SP280	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10757641	0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1178258	0.83[YRI][hapmap]
rs13298110	0.95[ASN][1000 genomes]
rs2181031	0.90[AFR][1000 genomes]
rs2224530	0.88[CHB][hapmap];0.81[AMR][1000 genomes]
rs2273723	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2273724	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2756900	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3117638	0.87[AMR][1000 genomes]
rs35417610	0.82[ASN][1000 genomes]
rs489451	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs489552	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536482	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs541065	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs542913	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs558931	0.83[AFR][1000 genomes]
rs566490	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs574118	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs581724	0.88[CHB][hapmap]
rs590894	0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs591831	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs593621	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs594949	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs595303	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs607650	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs608416	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs608934	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs609766	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs633903	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs638189	1.00[YRI][hapmap]
rs685421	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs685434	0.86[AFR][1000 genomes]
rs927370	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs927371	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv6512	chr9:27155677-27200455	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1009235	chr9:27189804-27196618	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs578327	TEK	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27165400-27198200	Weak transcription	Ovary	ovary
3	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:27166200-27205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:27178400-27197200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:27182600-27194000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:27184000-27197800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:27184200-27194000	Weak transcription	Psoas Muscle	Psoas
11	chr9:27184200-27212600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:27192000-27196800	Enhancers	HUVEC	blood vessel
13	chr9:27192200-27194200	Weak transcription	Osteobl	bone
14	chr9:27192400-27194600	Weak transcription	NHLF	lung
15	chr9:27192800-27194800	Weak transcription	Right Atrium	heart
16	chr9:27193000-27194000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:27193000-27194000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:27193000-27194000	Weak transcription	HSMM	muscle
19	chr9:27193000-27194200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:27193000-27194200	Weak transcription	HSMMtube	muscle
21	chr9:27193000-27195000	Weak transcription	Placenta	Placenta
22	chr9:27193000-27203000	Weak transcription	Aorta	Aorta
23	chr9:27193000-27204800	Weak transcription	Lung	lung
24	chr9:27193000-27209000	Weak transcription	Fetal Stomach	stomach
25	chr9:27193000-27212600	Weak transcription	Spleen	Spleen
26	chr9:27193000-27220000	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:27193200-27194200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:27193400-27194800	Weak transcription	Left Ventricle	heart
29	chr9:27193400-27195400	Enhancers	Colon Smooth Muscle	Colon
30	chr9:27193400-27202600	Weak transcription	Adipose Nuclei	Adipose
31	chr9:27193600-27195400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:27193800-27194200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:27193800-27195400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:27193800-27195400	Enhancers	HMEC	breast
35	chr9:27193800-27195600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:27193800-27195800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr9:27193800-27197200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:27193800-27197200	Enhancers	NHEK	skin
39	chr9:27193800-27197400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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