Variant report

Variant	rs17407149
Chromosome Location	chr8:19274848-19274849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19272075..19274991-chr8:19275738..19277539,3	MCF-7	breast:
2	chr8:19271313..19275229-chr8:19613615..19615862,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11204040	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11204041	0.80[YRI][hapmap]
rs11780343	0.92[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11782540	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11785649	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs11787230	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs12542575	0.88[YRI][hapmap]
rs12543061	0.92[ASW][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12674938	0.95[YRI][hapmap]
rs12675717	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12678336	0.81[AFR][1000 genomes]
rs12679712	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs13258090	0.93[MKK][hapmap]
rs13278459	0.95[YRI][hapmap]
rs17407039	0.85[EUR][1000 genomes]
rs4256608	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4333618	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs4391454	0.81[YRI][hapmap]
rs4392915	0.96[YRI][hapmap]
rs4412390	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs4430112	0.86[AFR][1000 genomes]
rs4431609	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4481612	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4549789	0.81[AFR][1000 genomes]
rs4554480	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4921638	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs4921642	0.81[AFR][1000 genomes]
rs4922028	0.84[MKK][hapmap];0.96[YRI][hapmap]
rs4922029	0.84[YRI][hapmap]
rs6981898	0.96[YRI][hapmap]
rs6983973	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6984145	0.86[AFR][1000 genomes]
rs6991231	0.88[EUR][1000 genomes]
rs6992893	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6997164	0.85[EUR][1000 genomes]
rs6999786	0.92[ASW][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap]
rs7006702	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7821446	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7823194	0.86[AFR][1000 genomes]
rs7833166	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
6	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv890622	chr8:19224772-19275354	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv610751	chr8:19226335-19284889	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv610752	chr8:19254816-19311496	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
15	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17407149	TNFRSF10A	cis	cerebellum	SCAN
rs17407149	CSGALNACT1	cis	cerebellum	SCAN
rs17407149	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx
rs17407149	CSGALNACT1	cis	parietal	SCAN
rs17407149	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19254000-19275000	Weak transcription	Gastric	stomach
2	chr8:19261800-19279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:19266600-19275200	Weak transcription	Right Ventricle	heart
4	chr8:19266600-19275400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr8:19266600-19283800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr8:19266800-19275200	Weak transcription	Spleen	Spleen
7	chr8:19267000-19275000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr8:19267000-19275000	Weak transcription	Aorta	Aorta
9	chr8:19267000-19278400	Weak transcription	Esophagus	oesophagus
10	chr8:19267000-19279200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:19267200-19297000	Weak transcription	Brain Substantia Nigra	brain
12	chr8:19267400-19279400	Weak transcription	Adipose Nuclei	Adipose
13	chr8:19267400-19280800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr8:19267400-19281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr8:19267400-19283600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:19267600-19281000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr8:19267800-19281800	Weak transcription	Brain Anterior Caudate	brain
18	chr8:19267800-19295600	Weak transcription	Brain Hippocampus Middle	brain
19	chr8:19268000-19279400	Weak transcription	Fetal Muscle Leg	muscle
20	chr8:19268000-19283800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr8:19269000-19276800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr8:19270000-19279600	Strong transcription	Primary B cells from cord blood	blood
23	chr8:19270200-19288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:19270400-19278800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr8:19270400-19283000	Weak transcription	Brain Angular Gyrus	brain
26	chr8:19271000-19284200	Weak transcription	Thymus	Thymus
27	chr8:19271200-19276000	Weak transcription	Brain Germinal Matrix	brain
28	chr8:19271400-19278600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr8:19271600-19275200	Weak transcription	Ovary	ovary
30	chr8:19271600-19281400	Weak transcription	Lung	lung
31	chr8:19271800-19275000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:19271800-19275000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr8:19271800-19279400	Weak transcription	Fetal Intestine Small	intestine
34	chr8:19271800-19281600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:19271800-19283400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr8:19271800-19305200	Weak transcription	Pancreas	Pancrea
37	chr8:19272000-19276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr8:19272200-19275000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr8:19272800-19281200	Weak transcription	Fetal Lung	lung
40	chr8:19273000-19277800	Strong transcription	Placenta	Placenta
41	chr8:19273200-19275000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr8:19273200-19275000	Weak transcription	Hela-S3	cervix
43	chr8:19273400-19276200	Strong transcription	A549	lung
44	chr8:19273600-19275000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr8:19274000-19277600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr8:19274000-19278600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr8:19274200-19275000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:19274200-19277600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr8:19274200-19278200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr8:19274400-19277600	Strong transcription	Fetal Stomach	stomach

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