Variant report

Variant	rs9987297
Chromosome Location	chr8:120933689-120933690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10092845	0.83[EUR][1000 genomes]
rs10099088	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955942	0.85[EUR][1000 genomes]
rs11984773	0.85[EUR][1000 genomes]
rs11984866	0.85[EUR][1000 genomes]
rs12541326	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12543242	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12545586	0.86[EUR][1000 genomes]
rs12548248	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12677306	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12679478	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13263147	0.86[EUR][1000 genomes]
rs13265513	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13265734	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13277786	0.90[EUR][1000 genomes]
rs13278508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13280041	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16893299	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1879149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2139430	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139431	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2176750	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2326432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461628	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28546392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600928	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35362581	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073559	0.85[EUR][1000 genomes]
rs4455866	0.82[ASN][1000 genomes]
rs4871010	0.86[EUR][1000 genomes]
rs4871011	0.86[EUR][1000 genomes]
rs4871786	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4871793	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4871795	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56177421	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62528673	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62528677	0.85[EUR][1000 genomes]
rs62528692	0.83[EUR][1000 genomes]
rs6469860	0.85[EUR][1000 genomes]
rs6469866	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6469869	0.83[EUR][1000 genomes]
rs6469873	0.80[EUR][1000 genomes]
rs6469875	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6469876	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6995862	0.83[EUR][1000 genomes]
rs6996081	0.83[EUR][1000 genomes]
rs6999911	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7000068	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7000488	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7004324	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7005888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7007672	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7018038	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7388491	0.87[EUR][1000 genomes]
rs7461170	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7462839	0.85[AFR][1000 genomes]
rs7813263	0.85[EUR][1000 genomes]
rs7813430	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7838578	0.86[EUR][1000 genomes]
rs7845043	0.87[EUR][1000 genomes]
rs869340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297607	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9649948	0.85[EUR][1000 genomes]
rs9649949	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9987135	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9987139	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9987140	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9987142	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9987165	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv972194	chr8:120898451-120965081	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1018953	chr8:120910380-120954832	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9987297	DSCC1	cis	Thyroid	GTEx
rs9987297	DSCC1	cis	Muscle Skeletal	GTEx
rs9987297	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs9987297	DSCC1	cis	lung	GTEx
rs9987297	DSCC1	cis	Nerve Tibial	GTEx
rs9987297	DEPTOR	cis	Esophagus Muscularis	GTEx
rs9987297	DSCC1	cis	Artery Aorta	GTEx
rs9987297	DSCC1	cis	Adipose Subcutaneous	GTEx
rs9987297	DSCC1	cis	Artery Tibial	GTEx
rs9987297	DSCC1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120923000-120935400	Enhancers	Stomach Mucosa	stomach
2	chr8:120926200-120944400	Weak transcription	Primary T cells from cord blood	blood
3	chr8:120927000-120934000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr8:120932000-120944800	Weak transcription	Aorta	Aorta
5	chr8:120932600-120934000	Enhancers	Gastric	stomach
6	chr8:120932800-120934000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr8:120932800-120936800	Enhancers	Brain Hippocampus Middle	brain
8	chr8:120932800-120940600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:120933000-120934800	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:120933000-120940800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:120933000-120941200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr8:120933000-120941400	Weak transcription	Fetal Lung	lung
13	chr8:120933000-120941600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr8:120933000-120944400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:120933000-120946000	Weak transcription	Placenta	Placenta
16	chr8:120933000-120948600	Weak transcription	Colonic Mucosa	Colon
17	chr8:120933000-120948800	Weak transcription	Esophagus	oesophagus
18	chr8:120933200-120934600	Weak transcription	Brain Angular Gyrus	brain
19	chr8:120933200-120934600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:120933200-120934800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:120933200-120934800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:120933200-120935000	Weak transcription	Ovary	ovary
23	chr8:120933200-120937000	Weak transcription	Fetal Stomach	stomach
24	chr8:120933200-120938400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:120933200-120940600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:120933200-120940600	Weak transcription	Liver	Liver
27	chr8:120933200-120941200	Weak transcription	Adipose Nuclei	Adipose
28	chr8:120933200-120941200	Weak transcription	Fetal Kidney	kidney
29	chr8:120933200-120941400	Weak transcription	Fetal Intestine Large	intestine
30	chr8:120933200-120941600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:120933200-120942000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr8:120933200-120942800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr8:120933200-120943200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr8:120933200-120944200	Weak transcription	Fetal Brain Female	brain
35	chr8:120933200-120946400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:120933200-120946600	Weak transcription	Lung	lung
37	chr8:120933200-120953600	Weak transcription	Right Ventricle	heart
38	chr8:120933400-120933800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:120933400-120934200	Weak transcription	Psoas Muscle	Psoas
40	chr8:120933400-120934800	Weak transcription	Brain Anterior Caudate	brain
41	chr8:120933400-120935200	Weak transcription	Spleen	Spleen
42	chr8:120933400-120937000	Weak transcription	Fetal Intestine Small	intestine
43	chr8:120933400-120941200	Weak transcription	Fetal Muscle Leg	muscle
44	chr8:120933600-120934600	Weak transcription	Brain Substantia Nigra	brain
45	chr8:120933600-120934600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr8:120933600-120935000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr8:120933600-120935000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:120933600-120935000	Weak transcription	Left Ventricle	heart
49	chr8:120933600-120935600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr8:120933600-120941200	Weak transcription	Fetal Muscle Trunk	muscle

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