Variant report

Variant	rs4150962
Chromosome Location	chr8:86122421-86122422
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	chr8:86088694..86090413-chr8:86121459..86123027,2	MCF-7	breast:
2	chr8:86115871..86119443-chr8:86120230..86123216,3	K562	blood:

Variant related genes	Relation type
ENSG00000260493	Chromatin interaction
ENSG00000133740	Chromatin interaction
ENSG00000254208	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10090196	0.81[EUR][1000 genomes]
rs10091577	0.81[EUR][1000 genomes]
rs10091582	0.81[ASN][1000 genomes]
rs10091710	0.82[EUR][1000 genomes]
rs10099251	0.81[ASN][1000 genomes]
rs10106970	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10111971	0.81[ASN][1000 genomes]
rs1021583	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11261469	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11261471	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12541299	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12541445	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12543256	0.88[ASN][1000 genomes]
rs12546106	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12550160	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12679400	0.86[ASN][1000 genomes]
rs13259464	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13269031	0.81[EUR][1000 genomes]
rs1553016	0.81[ASN][1000 genomes]
rs16913681	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16913721	0.82[EUR][1000 genomes]
rs17740658	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1845891	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1845892	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1908762	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2006767	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2132589	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132590	0.87[ASN][1000 genomes]
rs2279700	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279701	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291786	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403083	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2403084	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403085	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2403086	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28374336	0.81[ASN][1000 genomes]
rs28377260	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28439950	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28564613	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28677919	0.82[AFR][1000 genomes]
rs3779901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808538	0.82[ASN][1000 genomes]
rs4150865	0.81[EUR][1000 genomes]
rs4150867	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4150868	0.82[EUR][1000 genomes]
rs4150869	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4150884	0.83[EUR][1000 genomes]
rs4150893	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150897	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150909	0.88[ASN][1000 genomes]
rs4150942	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150944	0.89[ASN][1000 genomes]
rs4150964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150974	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150977	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4609189	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4617148	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4739698	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740045	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4740047	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62527173	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6605610	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6605611	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs67573812	0.80[ASN][1000 genomes]
rs6990449	0.80[ASN][1000 genomes]
rs6990452	0.80[ASN][1000 genomes]
rs6993316	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6994113	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7001359	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7004871	0.82[EUR][1000 genomes]
rs7011001	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7821629	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7827175	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7829240	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7839129	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7842013	0.82[EUR][1000 genomes]
rs9329908	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4150962	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs4150962	LRRCC1	cis	Artery Tibial	GTEx
rs4150962	LRRCC1	cis	Esophagus Mucosa	GTEx
rs4150962	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

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	chr8:86091600-86124200	Weak transcription	Primary T cells from cord blood	blood
6	chr8:86091600-86126000	Weak transcription	Hela-S3	cervix
7	chr8:86091800-86124200	Weak transcription	HMEC	breast
8	chr8:86101000-86122600	Weak transcription	Fetal Intestine Small	intestine
9	chr8:86101000-86124600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:86101000-86127800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:86101200-86127800	Weak transcription	Spleen	Spleen
12	chr8:86101200-86131000	Weak transcription	HepG2	liver
13	chr8:86102600-86125000	Weak transcription	Fetal Stomach	stomach
14	chr8:86102600-86125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:86102600-86128200	Weak transcription	Fetal Brain Male	brain
16	chr8:86110400-86128200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr8:86110600-86126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr8:86111000-86128000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr8:86113000-86127800	Weak transcription	Esophagus	oesophagus
20	chr8:86113200-86123000	Weak transcription	Fetal Brain Female	brain
21	chr8:86113200-86124200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr8:86113200-86124400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:86113200-86124400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr8:86113200-86124600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr8:86113200-86124800	Weak transcription	Brain Anterior Caudate	brain
26	chr8:86113200-86127600	Weak transcription	Right Ventricle	heart
27	chr8:86113200-86131200	Weak transcription	Fetal Heart	heart
28	chr8:86113400-86123200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr8:86113400-86124000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr8:86113400-86124000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr8:86113400-86124000	Weak transcription	Left Ventricle	heart
32	chr8:86113400-86124200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:86113400-86124400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr8:86113400-86124800	Weak transcription	Osteobl	bone
35	chr8:86113400-86125600	Weak transcription	NHDF-Ad	bronchial
36	chr8:86113400-86125800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:86113400-86128000	Weak transcription	Colon Smooth Muscle	Colon
38	chr8:86113400-86132000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr8:86113600-86128000	Weak transcription	Brain Hippocampus Middle	brain
40	chr8:86114200-86131200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:86114400-86131200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr8:86114800-86130600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr8:86116000-86123200	Weak transcription	Thymus	Thymus
44	chr8:86117000-86125800	Weak transcription	NHLF	lung
45	chr8:86118000-86124800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr8:86118200-86126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr8:86118400-86127000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr8:86118800-86124200	Weak transcription	NH-A	brain
49	chr8:86118800-86127600	Weak transcription	Lung	lung
50	chr8:86118800-86127600	Weak transcription	Small Intestine	intestine

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