Variant report

Variant	rs2896453
Chromosome Location	chr8:86106269-86106270
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86086301..86088008-chr8:86103625..86106550,2	K562	blood:
2	chr8:86019506..86022403-chr8:86104968..86106791,2	K562	blood:

Variant related genes	Relation type
ENSG00000133739	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10090196	0.83[ASN][1000 genomes]
rs13259399	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16913721	0.81[ASN][1000 genomes]
rs2278459	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2403082	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2403083	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2403084	0.83[ASN][1000 genomes]
rs2403085	0.81[ASN][1000 genomes]
rs2403086	0.81[ASN][1000 genomes]
rs2403087	0.81[AMR][1000 genomes]
rs2403089	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2896452	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808538	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150862	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4150893	0.83[ASN][1000 genomes]
rs4150897	0.83[ASN][1000 genomes]
rs4150942	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4739700	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4740043	0.80[ASN][1000 genomes]
rs4740044	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62527225	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6605609	0.83[ASN][1000 genomes]
rs6605624	0.87[AMR][1000 genomes]
rs6605625	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67573812	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6986704	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6987641	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6990256	0.84[AMR][1000 genomes]
rs6990449	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6990452	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6993387	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7007304	0.88[AMR][1000 genomes]
rs72682904	0.84[AMR][1000 genomes]
rs7818090	0.81[ASN][1000 genomes]
rs7818163	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7837275	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7838900	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv971329	chr8:86094967-86183119	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2896453	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs2896453	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2896453	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86090800-86127800	Weak transcription	Aorta	Aorta
2	chr8:86091000-86127800	Weak transcription	HSMMtube	muscle
3	chr8:86091000-86132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:86091200-86125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:86091600-86107600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:86091600-86107800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:86091600-86110000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:86091600-86124200	Weak transcription	Primary T cells from cord blood	blood
9	chr8:86091600-86126000	Weak transcription	Hela-S3	cervix
10	chr8:86091800-86124200	Weak transcription	HMEC	breast
11	chr8:86096200-86108400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr8:86096200-86121400	Weak transcription	Fetal Lung	lung
13	chr8:86096400-86107800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr8:86096400-86121400	Weak transcription	A549	lung
15	chr8:86096600-86120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr8:86096800-86109600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr8:86096800-86113000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:86098000-86112800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr8:86100400-86121400	Weak transcription	Fetal Intestine Large	intestine
20	chr8:86101000-86122600	Weak transcription	Fetal Intestine Small	intestine
21	chr8:86101000-86124600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr8:86101000-86127800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:86101200-86127800	Weak transcription	Spleen	Spleen
24	chr8:86101200-86131000	Weak transcription	HepG2	liver
25	chr8:86102600-86108800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr8:86102600-86108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr8:86102600-86112800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr8:86102600-86113600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:86102600-86121000	Weak transcription	Fetal Muscle Leg	muscle
30	chr8:86102600-86121600	Weak transcription	Dnd41	blood
31	chr8:86102600-86125000	Weak transcription	Fetal Stomach	stomach
32	chr8:86102600-86125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr8:86102600-86128200	Weak transcription	Fetal Brain Male	brain
34	chr8:86102800-86112800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:86103200-86113000	Weak transcription	Fetal Thymus	thymus
36	chr8:86103200-86118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr8:86103200-86120800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:86103600-86108600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr8:86104000-86113200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:86105000-86106800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:86106000-86107200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr8:86106000-86108800	Enhancers	Primary B cells from cord blood	blood
43	chr8:86106000-86110000	Weak transcription	GM12878-XiMat	blood
44	chr8:86106000-86112800	Weak transcription	Right Ventricle	heart
45	chr8:86106000-86120800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr8:86106200-86106800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr8:86106200-86107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:86106200-86112800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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