Variant report

Variant	rs28520356
Chromosome Location	chr8:8887153-8887154
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8887023..8887982-chr8:9195505..9196570,5	K562	blood:
2	chr8:8887010..8887803-chr8:9008211..9008746,2	MCF-7	breast:
3	chr8:8887049..8888008-chr8:9007777..9008961,10	K562	blood:
4	chr8:8886740..8888994-chr8:8890137..8892927,2	K562	blood:
5	chr8:8886723..8887985-chr8:9195522..9196377,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10091588	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036082	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774244	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775788	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779660	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779804	1.00[ASN][1000 genomes]
rs11780338	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780774	1.00[ASN][1000 genomes]
rs11781203	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782835	0.84[AMR][1000 genomes]
rs11784750	1.00[ASN][1000 genomes]
rs13250781	1.00[ASN][1000 genomes]
rs13277114	1.00[ASN][1000 genomes]
rs1530484	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17646197	1.00[ASN][1000 genomes]
rs17700611	1.00[ASN][1000 genomes]
rs17701980	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510464	0.91[EUR][1000 genomes]
rs28572014	1.00[ASN][1000 genomes]
rs34293316	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4840376	1.00[ASN][1000 genomes]
rs4840391	1.00[ASN][1000 genomes]
rs55824072	1.00[ASN][1000 genomes]
rs56109025	1.00[ASN][1000 genomes]
rs56349323	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400435	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57280925	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59041878	1.00[ASN][1000 genomes]
rs59257214	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60551984	1.00[ASN][1000 genomes]
rs61397430	1.00[ASN][1000 genomes]
rs61730232	1.00[ASN][1000 genomes]
rs62492947	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62493174	1.00[ASN][1000 genomes]
rs62495491	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62495539	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981610	1.00[ASN][1000 genomes]
rs6981745	1.00[ASN][1000 genomes]
rs6982619	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987569	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996374	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6998594	0.89[EUR][1000 genomes]
rs7001187	1.00[ASN][1000 genomes]
rs73518330	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73518392	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357482	1.00[ASN][1000 genomes]
rs73662247	1.00[ASN][1000 genomes]
rs7822129	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826478	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828944	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830266	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843024	1.00[ASN][1000 genomes]
rs7843154	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843369	1.00[ASN][1000 genomes]
rs7843789	1.00[ASN][1000 genomes]
rs7846007	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895253	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329175	1.00[ASN][1000 genomes]
rs9329176	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987276	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28520356	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861200-8892400	Weak transcription	Aorta	Aorta
2	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8861800-8887200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:8861800-8887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr8:8861800-8890000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
7	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
9	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:8861800-8892200	Weak transcription	Ovary	ovary
11	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
12	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
14	chr8:8870600-8892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:8871400-8892800	Weak transcription	HSMMtube	muscle
17	chr8:8871800-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr8:8871800-8894400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr8:8872000-8891200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:8872400-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:8875000-8891200	Weak transcription	Fetal Intestine Small	intestine
22	chr8:8875200-8887200	Weak transcription	Brain Substantia Nigra	brain
23	chr8:8875200-8897200	Weak transcription	Gastric	stomach
24	chr8:8875400-8890200	Weak transcription	Fetal Stomach	stomach
25	chr8:8875400-8892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr8:8875400-8894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr8:8875400-8897000	Weak transcription	Lung	lung
28	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
29	chr8:8875600-8890000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:8875600-8890200	Weak transcription	HSMM	muscle
31	chr8:8875800-8892200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr8:8876400-8887200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr8:8876400-8890000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr8:8876400-8898000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr8:8876800-8890000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr8:8876800-8891400	Weak transcription	Fetal Brain Female	brain
37	chr8:8877000-8894600	Weak transcription	HMEC	breast
38	chr8:8877000-8895600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr8:8877200-8895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:8878600-8890200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr8:8878800-8890200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr8:8879000-8890000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr8:8879200-8892600	Weak transcription	Osteobl	bone
45	chr8:8879400-8894200	Weak transcription	HepG2	liver
46	chr8:8879600-8887200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr8:8880000-8890000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:8880600-8890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:8880800-8887200	Weak transcription	NHEK	skin
50	chr8:8881000-8900400	Weak transcription	NH-A	brain

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