Variant report

Variant	rs17481249
Chromosome Location	chr8:19544426-19544427
allele	A/C
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	NFYB	chr8:19544370-19544742	GM12878	blood:	n/a	chr8:19544706-19544716
2	JUND	chr8:19544193-19544496	HepG2	liver:	n/a	chr8:19544340-19544349
3	NR3C1	chr8:19544104-19544472	A549	lung:	n/a	chr8:19544271-19544292
4	NR3C1	chr8:19544032-19544523	A549	lung:	n/a	chr8:19544271-19544292
5	RFX5	chr8:19544273-19544457	HepG2	liver:	n/a	n/a
6	CEBPB	chr8:19544228-19544963	IMR90	lung:	n/a	n/a
7	JUN	chr8:19544227-19544427	HepG2	liver:	n/a	chr8:19544336-19544349 chr8:19544340-19544349
8	RAD21	chr8:19544061-19544974	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
CSGALNACT1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10087018	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11990161	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12543757	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17481235	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994789	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1994790	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28680503	0.81[EUR][1000 genomes]
rs34674826	0.83[ASN][1000 genomes]
rs35486444	0.86[ASN][1000 genomes]
rs3735954	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735955	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4921665	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4921666	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4921668	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4922084	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4922086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4922087	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4922088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4990627	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6985674	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923765	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9987105	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong 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 miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv465602	chr8:19536015-19555398	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv610757	chr8:19536015-19555398	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv465603	chr8:19537084-19555398	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv465604	chr8:19537084-19555398	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv465606	chr8:19537084-19555398	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv465607	chr8:19537084-19555398	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv470203	chr8:19537084-19555398	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv610758	chr8:19537084-19555398	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17481249	CNOT7	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19539400-19552000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr8:19539600-19548200	Weak transcription	Brain Anterior Caudate	brain
3	chr8:19540200-19548000	Weak transcription	Hela-S3	cervix
4	chr8:19540400-19549000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:19540600-19548400	Weak transcription	Gastric	stomach
6	chr8:19540800-19545000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr8:19540800-19548400	Weak transcription	Ovary	ovary
8	chr8:19540800-19548600	Weak transcription	Right Ventricle	heart
9	chr8:19540800-19550400	Weak transcription	Lung	lung
10	chr8:19540800-19550400	Weak transcription	Spleen	Spleen
11	chr8:19541000-19554200	Weak transcription	Brain Substantia Nigra	brain
12	chr8:19541000-19567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:19542200-19545600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr8:19542200-19549000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:19542400-19546000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr8:19542400-19551000	Weak transcription	Fetal Brain Male	brain
17	chr8:19542800-19544600	Enhancers	Pancreas	Pancrea
18	chr8:19542800-19545800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr8:19542800-19546000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr8:19543000-19544800	Enhancers	Primary B cells from peripheral blood	blood
21	chr8:19543000-19548400	Weak transcription	Left Ventricle	heart
22	chr8:19543200-19545800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr8:19543200-19546400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr8:19543400-19544800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:19543400-19546600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr8:19543400-19548600	Weak transcription	Placenta	Placenta
27	chr8:19543600-19544600	Weak transcription	A549	lung
28	chr8:19543600-19546200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr8:19543800-19545200	Enhancers	Osteobl	bone
30	chr8:19544200-19544600	Enhancers	Primary T cells from cord blood	blood
31	chr8:19544200-19545000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr8:19544200-19548000	Weak transcription	Primary B cells from cord blood	blood
33	chr8:19544200-19548400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr8:19544200-19548600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr8:19544400-19545000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr8:19544400-19548600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr8:19544400-19550200	Weak transcription	Primary T cells fromperipheralblood	blood

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