Variant report

Variant	rs17090692
Chromosome Location	chr8:19540660-19540661
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	GATA3	chr8:19540096-19540750	SH-SY5Y	brain:	n/a	chr8:19540311-19540328 chr8:19540320-19540329
2	POLR2A	chr8:19538316-19541049	IMR90	lung:	n/a	n/a
3	GATA3	chr8:19540269-19540724	MCF-7	breast:	n/a	chr8:19540311-19540328 chr8:19540320-19540329
4	NR2F2	chr8:19540297-19540868	MCF-7	breast:	n/a	n/a
5	GATA2	chr8:19539931-19540976	SH-SY5Y	brain:	n/a	chr8:19540311-19540328 chr8:19540320-19540329

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19535486..19538060-chr8:19539195..19541920,3	K562	blood:
2	chr8:19535666..19538060-chr8:19539355..19541920,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD3-3	chr8:19540439-19540751	NONHSAT125377

Variant related genes	Relation type
CSGALNACT1	TF binding region
ENSG00000253270	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11204064	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11985450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11993323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17090675	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17090706	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17128819	1.00[CEU][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs55657185	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842263	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs55930732	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55990252	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56018532	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56373220	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58653515	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59187853	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60737109	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61450090	0.84[EUR][1000 genomes]
rs73216643	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7816924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	nsv890628	chr8:19527536-19540966	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
rs17090692	TNFRSF10D	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19536200-19540800	Enhancers	Pancreas	Pancrea
2	chr8:19536400-19543600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr8:19537600-19541000	Genic enhancers	A549	lung
4	chr8:19538400-19541200	Enhancers	Fetal Heart	heart
5	chr8:19538400-19541400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr8:19538600-19541000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:19538800-19540800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr8:19538800-19540800	Enhancers	Lung	lung
9	chr8:19538800-19541000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr8:19538800-19541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:19538800-19541000	Enhancers	HMEC	breast
12	chr8:19539000-19540800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr8:19539000-19540800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr8:19539000-19540800	Enhancers	Ovary	ovary
15	chr8:19539000-19541000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr8:19539000-19541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:19539200-19541000	Enhancers	Fetal Brain Female	brain
18	chr8:19539200-19542200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:19539400-19540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:19539400-19540800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr8:19539400-19540800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr8:19539400-19552000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr8:19539600-19540800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:19539600-19540800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:19539600-19541000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr8:19539600-19541000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:19539600-19541200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr8:19539600-19541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:19539600-19548200	Weak transcription	Brain Anterior Caudate	brain
30	chr8:19539800-19540800	Flanking Active TSS	Left Ventricle	heart
31	chr8:19540000-19540800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr8:19540200-19540800	Enhancers	Primary T cells from cord blood	blood
33	chr8:19540200-19540800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr8:19540200-19540800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr8:19540200-19540800	Flanking Active TSS	Right Ventricle	heart
36	chr8:19540200-19540800	Enhancers	Spleen	Spleen
37	chr8:19540200-19541000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:19540200-19541000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:19540200-19541000	Enhancers	Brain Substantia Nigra	brain
40	chr8:19540200-19548000	Weak transcription	Hela-S3	cervix
41	chr8:19540400-19540800	Bivalent Enhancer	Stomach Mucosa	stomach
42	chr8:19540400-19542000	Weak transcription	Fetal Brain Male	brain
43	chr8:19540400-19542200	Enhancers	Right Atrium	heart
44	chr8:19540400-19542800	Weak transcription	Aorta	Aorta
45	chr8:19540400-19543000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr8:19540400-19549000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:19540600-19540800	Genic enhancers	Primary B cells from cord blood	blood
48	chr8:19540600-19540800	Enhancers	Placenta	Placenta
49	chr8:19540600-19540800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr8:19540600-19540800	Enhancers	NH-A	brain

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