Variant report

Variant	rs4740044
Chromosome Location	chr8:86156680-86156681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86132667..86134494-chr8:86156330..86158323,2	K562	blood:
2	chr8:86088395..86090323-chr8:86154916..86157479,2	K562	blood:

Variant related genes	Relation type
ENSG00000260493	Chromatin interaction
ENSG00000185015	Chromatin interaction
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10088120	0.86[JPT][hapmap]
rs10090196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10106970	0.80[ASN][1000 genomes]
rs1014303	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1021583	0.91[JPT][hapmap]
rs11261468	0.95[JPT][hapmap]
rs11261471	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11261472	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11261474	0.91[JPT][hapmap]
rs11985733	0.91[JPT][hapmap]
rs11989660	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12114575	0.83[ASN][1000 genomes]
rs12541445	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12543256	0.91[JPT][hapmap]
rs12544332	0.82[JPT][hapmap]
rs12546106	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12550160	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1303806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1303807	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13252971	0.91[JPT][hapmap]
rs13259399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13269739	0.86[JPT][hapmap]
rs1390711	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1493302	0.91[JPT][hapmap]
rs1496529	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496530	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496531	0.81[JPT][hapmap]
rs1496532	0.81[JPT][hapmap]
rs1532423	0.86[JPT][hapmap]
rs1532424	0.91[JPT][hapmap]
rs1553015	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16913681	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs16913721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17740658	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1908762	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1995056	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995057	0.86[JPT][hapmap]
rs1995058	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2006767	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2055077	0.86[JPT][hapmap]
rs20571	0.91[JPT][hapmap]
rs2072696	0.90[JPT][hapmap]
rs2132589	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2278459	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2279701	0.86[JPT][hapmap]
rs2291786	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2291787	0.86[JPT][hapmap]
rs2403083	0.86[JPT][hapmap]
rs2403085	0.87[JPT][hapmap]
rs2403086	0.86[JPT][hapmap]
rs2403088	0.95[JPT][hapmap]
rs2403104	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2548281	0.86[JPT][hapmap]
rs2645049	0.86[JPT][hapmap]
rs28564613	0.82[ASN][1000 genomes]
rs28677919	0.97[ASN][1000 genomes]
rs2896452	0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs2896453	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2896454	0.86[JPT][hapmap]
rs34103685	0.86[JPT][hapmap]
rs35285802	0.84[ASN][1000 genomes]
rs3779899	0.86[JPT][hapmap]
rs3779901	0.91[JPT][hapmap]
rs3808538	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808539	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3808540	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs4150867	0.87[JPT][hapmap]
rs4150868	0.86[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.86[JPT][hapmap]
rs4150909	0.86[JPT][hapmap]
rs4150942	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4150944	0.86[JPT][hapmap]
rs4150964	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4150974	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4150977	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4609189	0.91[JPT][hapmap]
rs4739700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4739702	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4740043	0.91[JPT][hapmap]
rs4740045	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4740048	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4740049	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62527225	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6605610	0.91[JPT][hapmap]
rs6605611	0.90[JPT][hapmap]
rs6605624	0.95[JPT][hapmap];0.90[YRI][hapmap]
rs67573812	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6987641	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6990449	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6990452	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6993387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6994113	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6997458	0.86[JPT][hapmap]
rs7001359	0.86[JPT][hapmap]
rs7004871	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7008772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7011001	0.82[ASN][1000 genomes]
rs7011926	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7015758	0.87[JPT][hapmap]
rs725605	0.81[JPT][hapmap]
rs7818163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7821629	0.81[ASN][1000 genomes]
rs7826589	0.91[JPT][hapmap]
rs7827175	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7829050	0.87[JPT][hapmap]
rs7829144	0.95[JPT][hapmap]
rs7829240	0.80[ASN][1000 genomes]
rs7833737	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7835303	0.83[ASN][1000 genomes]
rs7835882	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7837275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7838900	0.80[AMR][1000 genomes]
rs7841142	0.95[JPT][hapmap]
rs903895	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs903896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903897	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs931505	0.87[JPT][hapmap]
rs9987281	0.91[JPT][hapmap]

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	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
2	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2761441	chr8:86155592-86167129	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4740044	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs4740044	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs4740044	LRRCC1	cis	Esophagus Mucosa	GTEx
rs4740044	CA13	cis	Lymphoblastoid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86133800-86157200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:86134600-86157200	Weak transcription	Right Atrium	heart
3	chr8:86136000-86157200	Weak transcription	Liver	Liver
4	chr8:86136200-86157000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:86136400-86157000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr8:86139600-86157200	Weak transcription	Pancreas	Pancrea
7	chr8:86142600-86157200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:86143600-86157000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:86145000-86157200	Weak transcription	Ovary	ovary
10	chr8:86145600-86157400	Weak transcription	Brain Angular Gyrus	brain
11	chr8:86146200-86157200	Weak transcription	Gastric	stomach
12	chr8:86148000-86157200	Weak transcription	Esophagus	oesophagus
13	chr8:86148200-86157200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:86149200-86157000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr8:86152000-86157200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr8:86152400-86157200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:86152600-86157000	Weak transcription	Stomach Mucosa	stomach
18	chr8:86152800-86157200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:86153000-86157000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:86153200-86157000	Weak transcription	Fetal Intestine Large	intestine
21	chr8:86153200-86157200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:86154000-86157000	Weak transcription	Fetal Intestine Small	intestine
23	chr8:86154600-86157200	Weak transcription	HepG2	liver
24	chr8:86155000-86156800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr8:86156000-86157200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:86156200-86156800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr8:86156600-86157200	Weak transcription	Thymus	Thymus

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