Variant report

Variant	rs28461628
Chromosome Location	chr8:120940867-120940868
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	chr8:120940406..120942141-chr8:120945749..120947949,2	K562	blood:
2	chr8:120939661..120942312-chr8:120943656..120945414,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10099088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955942	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11984773	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11984866	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12541326	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12543242	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12545586	0.83[EUR][1000 genomes]
rs12548248	0.84[EUR][1000 genomes]
rs12677306	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12679478	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13263147	0.82[EUR][1000 genomes]
rs13265513	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13265734	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13277786	0.86[EUR][1000 genomes]
rs13278508	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13280041	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16893299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879149	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2002377	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2017310	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056305	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2139430	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176750	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326432	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28546392	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28600928	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35362581	0.86[EUR][1000 genomes]
rs4073559	0.82[EUR][1000 genomes]
rs4871010	0.82[EUR][1000 genomes]
rs4871011	0.82[EUR][1000 genomes]
rs4871786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56177421	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62528673	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62528677	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62528692	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6469860	0.82[EUR][1000 genomes]
rs6469866	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6469869	0.82[EUR][1000 genomes]
rs6469875	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6469876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6995862	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6996081	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6999911	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7000068	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7000488	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7004324	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7005888	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7007672	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7018038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388491	0.84[EUR][1000 genomes]
rs7461170	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7462839	0.80[AFR][1000 genomes]
rs7813263	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7813430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838578	0.82[EUR][1000 genomes]
rs7845043	0.84[EUR][1000 genomes]
rs869340	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869341	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9297607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649948	0.82[EUR][1000 genomes]
rs9649949	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9987135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987139	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987142	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987165	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9987297	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28461628	DSCC1	cis	Artery Tibial	GTEx
rs28461628	DSCC1	cis	Thyroid	GTEx
rs28461628	DSCC1	cis	Esophagus Muscularis	GTEx
rs28461628	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs28461628	DSCC1	cis	Nerve Tibial	GTEx
rs28461628	DEPTOR	cis	Esophagus Muscularis	GTEx
rs28461628	DSCC1	cis	Adipose Subcutaneous	GTEx
rs28461628	DSCC1	cis	Muscle Skeletal	GTEx
rs28461628	DSCC1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120926200-120944400	Weak transcription	Primary T cells from cord blood	blood
2	chr8:120932000-120944800	Weak transcription	Aorta	Aorta
3	chr8:120933000-120941200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:120933000-120941400	Weak transcription	Fetal Lung	lung
5	chr8:120933000-120941600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr8:120933000-120944400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:120933000-120946000	Weak transcription	Placenta	Placenta
8	chr8:120933000-120948600	Weak transcription	Colonic Mucosa	Colon
9	chr8:120933000-120948800	Weak transcription	Esophagus	oesophagus
10	chr8:120933200-120941200	Weak transcription	Adipose Nuclei	Adipose
11	chr8:120933200-120941200	Weak transcription	Fetal Kidney	kidney
12	chr8:120933200-120941400	Weak transcription	Fetal Intestine Large	intestine
13	chr8:120933200-120941600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr8:120933200-120942000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr8:120933200-120942800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:120933200-120943200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr8:120933200-120944200	Weak transcription	Fetal Brain Female	brain
18	chr8:120933200-120946400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr8:120933200-120946600	Weak transcription	Lung	lung
20	chr8:120933200-120953600	Weak transcription	Right Ventricle	heart
21	chr8:120933400-120941200	Weak transcription	Fetal Muscle Leg	muscle
22	chr8:120933600-120941200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:120933600-120942800	Weak transcription	Pancreas	Pancrea
24	chr8:120934000-120942600	Weak transcription	Gastric	stomach
25	chr8:120934000-120950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr8:120935400-120959200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr8:120935800-120941000	Weak transcription	Left Ventricle	heart
28	chr8:120935800-120963200	Weak transcription	Psoas Muscle	Psoas
29	chr8:120937600-120942400	Weak transcription	Fetal Intestine Small	intestine
30	chr8:120937600-120942400	Weak transcription	Fetal Stomach	stomach
31	chr8:120937800-120946800	Weak transcription	Stomach Mucosa	stomach
32	chr8:120939000-120941600	Weak transcription	Brain Angular Gyrus	brain
33	chr8:120939400-120948400	Weak transcription	Brain Anterior Caudate	brain
34	chr8:120939600-120941400	Weak transcription	Brain Hippocampus Middle	brain
35	chr8:120939600-120946600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr8:120939600-120959200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr8:120940200-120944400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:120940200-120951000	Weak transcription	Osteobl	bone
39	chr8:120940400-120941000	Enhancers	Brain Substantia Nigra	brain
40	chr8:120940600-120942200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr8:120940600-120943600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr8:120940600-120944000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr8:120940600-120945600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr8:120940600-120947600	Strong transcription	Liver	Liver
45	chr8:120940600-120950200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr8:120940600-120950200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr8:120940800-120941600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr8:120940800-120944400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:120940800-120944600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr8:120940800-120944800	Strong transcription	Colon Smooth Muscle	Colon

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