Variant report

Variant	rs7829144
Chromosome Location	chr8:86028331-86028332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86019339..86022486-chr8:86024530..86028915,4	K562	blood:
2	chr8:86018746..86021962-chr8:86025376..86029734,4	K562	blood:
3	chr8:86023655..86027184-chr8:86028294..86031138,3	K562	blood:

Variant related genes	Relation type
ENSG00000133739	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10088120	0.80[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap]
rs10090196	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10100442	0.84[JPT][hapmap]
rs10104630	0.82[JPT][hapmap]
rs1021583	0.85[JPT][hapmap]
rs11261468	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11261471	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs12541445	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs12543256	0.85[JPT][hapmap]
rs12546106	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs12550160	0.85[JPT][hapmap]
rs13259399	0.95[JPT][hapmap];0.91[MEX][hapmap]
rs13269739	0.90[JPT][hapmap]
rs1553015	0.91[JPT][hapmap];0.92[MEX][hapmap]
rs16913600	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs16913681	0.85[JPT][hapmap]
rs16913721	0.95[JPT][hapmap];0.92[MEX][hapmap]
rs17740658	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs1851973	0.82[JPT][hapmap]
rs1908762	0.81[JPT][hapmap];0.91[MEX][hapmap]
rs2006767	0.95[JPT][hapmap];0.92[MEX][hapmap]
rs2132589	0.85[JPT][hapmap];0.83[MEX][hapmap]
rs2278459	0.87[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2279701	0.81[JPT][hapmap]
rs2291786	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs2403082	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403083	0.90[JPT][hapmap]
rs2403085	0.91[JPT][hapmap]
rs2403086	0.90[JPT][hapmap]
rs2403087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403088	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs2403089	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2896452	0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs2896454	0.80[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs34103685	0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs3779899	0.80[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs3779901	0.85[JPT][hapmap]
rs3808538	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs4150862	0.90[ASN][1000 genomes]
rs4150867	0.91[JPT][hapmap]
rs4150868	0.90[JPT][hapmap]
rs4150869	0.90[JPT][hapmap]
rs4150893	0.91[JPT][hapmap];0.92[MEX][hapmap]
rs4150909	0.91[JPT][hapmap]
rs4150942	0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4150944	0.91[JPT][hapmap]
rs4150964	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs4150974	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs4150977	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs4609189	0.85[JPT][hapmap]
rs4739700	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs4740043	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4740044	0.95[JPT][hapmap]
rs4740045	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs6605609	0.92[ASN][1000 genomes]
rs6605610	0.85[JPT][hapmap]
rs6605611	0.85[JPT][hapmap]
rs6605624	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6605625	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6986704	0.94[ASN][1000 genomes]
rs6990256	0.86[ASN][1000 genomes]
rs6990449	0.93[JPT][hapmap]
rs6993387	0.95[JPT][hapmap]
rs6994113	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs7001359	0.81[JPT][hapmap]
rs7008772	0.95[JPT][hapmap]
rs7015758	0.91[JPT][hapmap]
rs72682904	0.90[ASN][1000 genomes]
rs7814435	0.86[ASN][1000 genomes]
rs7818090	0.88[ASN][1000 genomes]
rs7818163	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs7826589	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7827175	0.85[JPT][hapmap];0.92[MEX][hapmap]
rs7829050	0.91[JPT][hapmap]
rs7838900	0.88[ASN][1000 genomes]
rs7841142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9692962	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1033160	chr8:86010643-86030560	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7829144	C8orf59	cis	parietal	SCAN
rs7829144	LRRCC1	cis	parietal	SCAN
rs7829144	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs7829144	LRRCC1	cis	cerebellum	SCAN
rs7829144	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs7829144	C8orf59	cis	cerebellum	SCAN
rs7829144	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020200-86032600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr8:86020200-86042200	Weak transcription	Left Ventricle	heart
4	chr8:86020400-86032400	Weak transcription	Fetal Thymus	thymus
5	chr8:86020400-86034400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr8:86020400-86043800	Weak transcription	NH-A	brain
7	chr8:86020400-86044400	Weak transcription	Fetal Muscle Leg	muscle
8	chr8:86020400-86048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:86020400-86048400	Weak transcription	Fetal Stomach	stomach
10	chr8:86020400-86049000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr8:86020400-86054800	Weak transcription	Lung	lung
12	chr8:86020400-86055400	Weak transcription	Fetal Kidney	kidney
13	chr8:86020400-86055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:86020400-86056400	Weak transcription	Gastric	stomach
15	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
16	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
17	chr8:86020600-86029400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr8:86020600-86031800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr8:86020600-86031800	Weak transcription	HMEC	breast
20	chr8:86020600-86032000	Weak transcription	NHEK	skin
21	chr8:86020600-86032400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:86020600-86034400	Weak transcription	Liver	Liver
23	chr8:86020600-86039200	Weak transcription	Adipose Nuclei	Adipose
24	chr8:86020600-86041600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr8:86020600-86044200	Weak transcription	Primary T cells from cord blood	blood
26	chr8:86020600-86045800	Weak transcription	Thymus	Thymus
27	chr8:86020600-86048800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr8:86020600-86049000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr8:86020600-86049200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:86020600-86052400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr8:86020600-86054600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:86020800-86039000	Weak transcription	Brain Hippocampus Middle	brain
34	chr8:86020800-86050600	Weak transcription	Brain Angular Gyrus	brain
35	chr8:86021000-86028600	Weak transcription	Fetal Heart	heart
36	chr8:86021000-86032000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:86021000-86034400	Weak transcription	Fetal Lung	lung
38	chr8:86021000-86039800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr8:86021000-86039800	Weak transcription	NHDF-Ad	bronchial
40	chr8:86021000-86046000	Weak transcription	Colon Smooth Muscle	Colon
41	chr8:86021000-86049800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr8:86021200-86034800	Weak transcription	GM12878-XiMat	blood
43	chr8:86021200-86035000	Weak transcription	Fetal Intestine Small	intestine
44	chr8:86021200-86039000	Weak transcription	Fetal Brain Female	brain
45	chr8:86021200-86053600	Weak transcription	Brain Substantia Nigra	brain
46	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
48	chr8:86021400-86041800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
50	chr8:86021600-86039600	Weak transcription	K562	blood

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