Variant report

Variant	rs2403088
Chromosome Location	chr8:86041844-86041845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86041361..86043204-chr8:86048252..86049988,2	MCF-7	breast:
2	chr8:86041424..86043525-chr8:86089868..86091412,2	MCF-7	breast:
3	chr8:86018609..86020657-chr8:86041368..86044315,2	K562	blood:

Variant related genes	Relation type
ENSG00000133739	Chromatin interaction
ENSG00000254208	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10088120	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10090196	0.95[JPT][hapmap];0.85[TSI][hapmap]
rs10091577	0.90[EUR][1000 genomes]
rs10091710	0.91[EUR][1000 genomes]
rs10100442	0.95[CEU][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10104630	0.82[JPT][hapmap]
rs1021583	0.85[JPT][hapmap]
rs11261468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs11261471	0.81[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12541445	0.81[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12543256	0.85[JPT][hapmap]
rs12546106	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs12550160	0.85[JPT][hapmap]
rs12926	0.85[EUR][1000 genomes]
rs13249364	0.92[EUR][1000 genomes]
rs13259399	0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs13269031	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs1553015	0.91[JPT][hapmap];0.88[MEX][hapmap]
rs16913600	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs16913681	0.85[JPT][hapmap]
rs16913721	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs17740658	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1908762	0.81[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2006767	0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2132589	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2278459	0.87[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2279701	0.81[JPT][hapmap]
rs2291786	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2291787	0.81[JPT][hapmap]
rs2403082	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2403083	0.90[JPT][hapmap]
rs2403084	0.81[EUR][1000 genomes]
rs2403085	0.86[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs2403086	0.86[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2403087	0.99[ASN][1000 genomes]
rs2403089	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403104	0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs28621707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2896452	0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.91[ASN][1000 genomes]
rs2896454	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34103685	0.82[CEU][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs3779899	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3779901	0.85[JPT][hapmap]
rs3808538	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs3808539	0.91[JPT][hapmap]
rs4150859	0.86[EUR][1000 genomes]
rs4150862	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150865	0.90[EUR][1000 genomes]
rs4150867	1.00[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150868	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs4150869	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150884	0.90[EUR][1000 genomes]
rs4150893	0.86[CEU][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4150897	0.81[EUR][1000 genomes]
rs4150909	0.91[JPT][hapmap]
rs4150942	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs4150944	0.91[JPT][hapmap]
rs4150964	0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4150974	0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4150977	0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs4609189	0.85[JPT][hapmap]
rs4739700	0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs4740043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740044	0.95[JPT][hapmap]
rs4740045	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs62527168	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62527173	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6605609	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6605610	0.85[JPT][hapmap]
rs6605611	0.85[JPT][hapmap]
rs6605624	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6605625	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986704	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6990256	0.89[ASN][1000 genomes]
rs6990449	0.93[JPT][hapmap]
rs6993387	0.95[JPT][hapmap]
rs6994113	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7001359	0.81[JPT][hapmap]
rs7004765	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7007304	0.81[ASN][1000 genomes]
rs7008032	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7008772	0.95[JPT][hapmap]
rs7010228	0.85[EUR][1000 genomes]
rs7015758	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72682904	0.92[ASN][1000 genomes]
rs7814435	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7818090	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7818163	0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7823218	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7826589	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7827175	0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7829050	1.00[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7829144	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]
rs7838900	0.91[ASN][1000 genomes]
rs7841142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7842013	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903895	0.91[JPT][hapmap]
rs903896	0.91[JPT][hapmap];0.88[MEX][hapmap]
rs903897	0.91[JPT][hapmap]
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	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
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2403088	LRRCC1	cis	uninvolved skin	skin_eQTL
rs2403088	LRRCC1	cis	lesional skin	skin_eQTL
rs2403088	LRRCC1	cis	cerebellum	SCAN
rs2403088	C8orf59	cis	cerebellum	SCAN
rs2403088	LRRCC1	cis	Artery Tibial	GTEx
rs2403088	C8orf59	cis	parietal	SCAN
rs2403088	LRRCC1	cis	Esophagus Mucosa	GTEx
rs2403088	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2403088	CA13	cis	cerebellum	SCAN
rs2403088	LRRCC1	cis	normal skin	skin_eQTL
rs2403088	LRRCC1	cis	parietal	SCAN
rs2403088	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020200-86042200	Weak transcription	Left Ventricle	heart
3	chr8:86020400-86043800	Weak transcription	NH-A	brain
4	chr8:86020400-86044400	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:86020400-86048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:86020400-86048400	Weak transcription	Fetal Stomach	stomach
7	chr8:86020400-86049000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr8:86020400-86054800	Weak transcription	Lung	lung
9	chr8:86020400-86055400	Weak transcription	Fetal Kidney	kidney
10	chr8:86020400-86055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:86020400-86056400	Weak transcription	Gastric	stomach
12	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
13	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
14	chr8:86020600-86044200	Weak transcription	Primary T cells from cord blood	blood
15	chr8:86020600-86045800	Weak transcription	Thymus	Thymus
16	chr8:86020600-86048800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr8:86020600-86049000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr8:86020600-86049200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:86020600-86052400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:86020600-86054600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr8:86020800-86050600	Weak transcription	Brain Angular Gyrus	brain
23	chr8:86021000-86046000	Weak transcription	Colon Smooth Muscle	Colon
24	chr8:86021000-86049800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr8:86021200-86053600	Weak transcription	Brain Substantia Nigra	brain
26	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
28	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
29	chr8:86021600-86049800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:86021800-86045200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:86025200-86057400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:86028600-86056400	Weak transcription	Ovary	ovary
34	chr8:86032400-86045800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr8:86032600-86050400	Weak transcription	HMEC	breast
36	chr8:86032800-86057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:86033000-86042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
39	chr8:86033600-86046000	Weak transcription	Colonic Mucosa	Colon
40	chr8:86033600-86049000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:86034600-86051200	Weak transcription	Liver	Liver
42	chr8:86035200-86043600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:86035200-86049000	Weak transcription	GM12878-XiMat	blood
44	chr8:86035200-86055600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:86035400-86045600	Weak transcription	Fetal Lung	lung
46	chr8:86036200-86049400	Weak transcription	HSMM	muscle
47	chr8:86036600-86050600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr8:86036800-86050400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
50	chr8:86037400-86056000	Weak transcription	Right Ventricle	heart

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