Variant report

Variant	rs3808538
Chromosome Location	chr8:86121311-86121312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86115871..86119443-chr8:86120230..86123216,3	K562	blood:
2	chr8:86119264..86121436-chr8:86127693..86129609,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10088120	0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs10090196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs10100442	0.87[TSI][hapmap]
rs10106970	0.80[ASN][1000 genomes]
rs1014303	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1021583	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11261468	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs11261471	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs11261472	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11261474	0.91[JPT][hapmap]
rs11989660	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12541445	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs12543256	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs12544332	0.81[JPT][hapmap]
rs12546106	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs12550160	0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1303806	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs1303807	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13252971	0.90[JPT][hapmap]
rs13259399	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13269739	0.86[JPT][hapmap]
rs1390711	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1496529	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496530	0.86[CHB][hapmap];0.98[CHD][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	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16913681	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16913721	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs17740658	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1908762	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1995056	0.82[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1995057	0.86[JPT][hapmap]
rs1995058	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs2006767	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs2132589	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs2278459	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279701	0.86[JPT][hapmap]
rs2291786	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.80[ASN][1000 genomes]
rs2291787	0.86[JPT][hapmap]
rs2403082	0.85[AMR][1000 genomes]
rs2403083	0.80[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2403085	0.86[JPT][hapmap]
rs2403086	0.86[JPT][hapmap]
rs2403088	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs2403089	0.86[AMR][1000 genomes]
rs2403104	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2548281	0.86[JPT][hapmap]
rs2645049	0.86[JPT][hapmap]
rs28677919	0.92[ASN][1000 genomes]
rs2896452	1.00[ASW][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2896453	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2896454	0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs34103685	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs35285802	0.80[ASN][1000 genomes]
rs3779899	0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs3779901	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3808539	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs3808540	0.82[GIH][hapmap]
rs4150867	0.86[JPT][hapmap]
rs4150868	0.86[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.86[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs4150909	0.86[JPT][hapmap]
rs4150942	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4150944	0.86[JPT][hapmap]
rs4150962	0.82[ASN][1000 genomes]
rs4150964	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs4150974	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs4150977	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs4609189	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4739700	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4739702	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740043	0.91[JPT][hapmap]
rs4740044	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]
rs4740045	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs4740048	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740049	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62527225	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6605610	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6605611	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6605624	1.00[ASW][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs6605625	0.85[AMR][1000 genomes]
rs67573812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6987641	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6990449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6990452	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6993387	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6994113	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs6997458	0.86[JPT][hapmap]
rs7001359	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7004871	0.85[ASN][1000 genomes]
rs7007304	0.83[AMR][1000 genomes]
rs7008772	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7011926	0.82[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7015758	0.86[JPT][hapmap]
rs725605	0.81[JPT][hapmap]
rs7818163	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7826589	0.91[JPT][hapmap]
rs7827175	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs7829050	0.86[JPT][hapmap]
rs7829144	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs7829240	0.80[ASN][1000 genomes]
rs7833737	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7835882	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7837275	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7838900	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7841142	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs903895	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs903896	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs903897	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3808538	LRRCC1	cis	brain	BrainEAC
rs3808538	CA13	cis	lymphoblastoid	seeQTL
rs3808538	LRRCC1	cis	lesional skin	skin_eQTL
rs3808538	LRRCC1	cis	Esophagus Mucosa	GTEx
rs3808538	C8orf59	cis	cerebellum	SCAN
rs3808538	C8orf59	cis	lymphoblastoid	seeQTL
rs3808538	C8orf59	cis	parietal	SCAN
rs3808538	LRRCC1	cis	parietal	SCAN
rs3808538	LRRCC1	cis	cerebellum	SCAN

Chromatin state (count:88 , 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	chr8:86096200-86121400	Weak transcription	Fetal Lung	lung
9	chr8:86096400-86121400	Weak transcription	A549	lung
10	chr8:86100400-86121400	Weak transcription	Fetal Intestine Large	intestine
11	chr8:86101000-86122600	Weak transcription	Fetal Intestine Small	intestine
12	chr8:86101000-86124600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:86101000-86127800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:86101200-86127800	Weak transcription	Spleen	Spleen
15	chr8:86101200-86131000	Weak transcription	HepG2	liver
16	chr8:86102600-86121600	Weak transcription	Dnd41	blood
17	chr8:86102600-86125000	Weak transcription	Fetal Stomach	stomach
18	chr8:86102600-86125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:86102600-86128200	Weak transcription	Fetal Brain Male	brain
20	chr8:86108200-86121400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:86110400-86128200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr8:86110600-86126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr8:86111000-86128000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:86113000-86127800	Weak transcription	Esophagus	oesophagus
25	chr8:86113200-86123000	Weak transcription	Fetal Brain Female	brain
26	chr8:86113200-86124200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr8:86113200-86124400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr8:86113200-86124400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr8:86113200-86124600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:86113200-86124800	Weak transcription	Brain Anterior Caudate	brain
31	chr8:86113200-86127600	Weak transcription	Right Ventricle	heart
32	chr8:86113200-86131200	Weak transcription	Fetal Heart	heart
33	chr8:86113400-86121600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr8:86113400-86123200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:86113400-86124000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr8:86113400-86124000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr8:86113400-86124000	Weak transcription	Left Ventricle	heart
38	chr8:86113400-86124200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr8:86113400-86124400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr8:86113400-86124800	Weak transcription	Osteobl	bone
41	chr8:86113400-86125600	Weak transcription	NHDF-Ad	bronchial
42	chr8:86113400-86125800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:86113400-86128000	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:86113400-86132000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr8:86113600-86128000	Weak transcription	Brain Hippocampus Middle	brain
46	chr8:86113800-86121400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr8:86113800-86121400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr8:86114200-86131200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:86114400-86131200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:86114800-86130600	Strong transcription	Primary B cells from peripheral blood	blood

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