Variant report

Variant	rs2403086
Chromosome Location	chr8:86113204-86113205
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr8:86112531-86113232	GM12878	blood:	n/a	n/a
2	NFIC	chr8:86112532-86113316	GM12878	blood:	n/a	n/a
3	SMC3	chr8:86112695-86113419	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr8:86112535-86113481	GM12878	blood:	n/a	n/a
5	WRNIP1	chr8:86112710-86113324	GM12878	blood:	n/a	n/a
6	RUNX3	chr8:86112520-86113239	GM12878	blood:	n/a	n/a
7	FOXM1	chr8:86112544-86113234	GM12878	blood:	n/a	n/a
8	ZNF143	chr8:86112717-86113323	GM12878	blood:	n/a	n/a
9	POLR2A	chr8:86112714-86113515	GM12891	blood:	n/a	n/a
10	STAT3	chr8:86112660-86113212	GM12878	blood:	n/a	chr8:86112901-86112912
11	NRF1	chr8:86113114-86113373	GM12878	blood:	n/a	n/a
12	MAX	chr8:86112680-86113379	GM12878	blood:	n/a	chr8:86112797-86112806
13	MTA3	chr8:86112588-86113328	GM12878	blood:	n/a	n/a
14	CHD2	chr8:86112641-86113228	GM12878	blood:	n/a	n/a
15	EBF1	chr8:86112602-86113505	GM12878	blood:	n/a	chr8:86112879-86112890
16	EP300	chr8:86112449-86113214	GM12878	blood:	n/a	n/a
17	POLR2A	chr8:86112676-86113561	GM12891	blood:	n/a	n/a
18	RUNX3	chr8:86112502-86113439	GM12878	blood:	n/a	n/a
19	CUX1	chr8:86112554-86113298	GM12878	blood:	n/a	n/a
20	STAT1	chr8:86112762-86113245	GM12878	blood:	n/a	chr8:86112901-86112912
21	RELA	chr8:86112701-86113572	GM19099	blood:	n/a	n/a
22	RCOR1	chr8:86112652-86113343	GM12878	blood:	n/a	n/a
23	PML	chr8:86112704-86113545	GM12878	blood:	n/a	n/a
24	CHD1	chr8:86112740-86113394	GM12878	blood:	n/a	n/a
25	POLR2A	chr8:86112732-86113466	GM12878	blood:	n/a	n/a
26	NFIC	chr8:86112564-86113278	GM12878	blood:	n/a	n/a
27	BCLAF1	chr8:86112598-86113205	GM12878	blood:	n/a	chr8:86112894-86112903

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86102705..86104394-chr8:86111397..86113431,2	K562	blood:
2	chr8:86111093..86113601-chr8:86113672..86116440,2	K562	blood:

Variant related genes	Relation type
E2F5	TF binding region
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10088120	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10090196	0.86[JPT][hapmap]
rs10091577	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10091710	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10100442	0.81[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10106970	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1021583	0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11261468	0.90[JPT][hapmap]
rs11261469	0.83[ASN][1000 genomes]
rs11261471	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12541445	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12543256	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12544332	0.86[JPT][hapmap]
rs12546106	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12550160	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12926	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1303806	0.82[JPT][hapmap]
rs13249364	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap]
rs13259464	0.82[ASN][1000 genomes]
rs13269031	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13269739	1.00[JPT][hapmap]
rs1390711	0.82[JPT][hapmap]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1553015	0.82[JPT][hapmap]
rs16913681	0.83[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16913721	0.86[JPT][hapmap]
rs17740658	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1845891	0.84[ASN][1000 genomes]
rs1845892	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1908762	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1995057	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1995058	0.82[JPT][hapmap]
rs2006767	0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2132589	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2132590	0.84[ASN][1000 genomes]
rs2278459	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279701	0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2291786	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291787	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2403083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2403084	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403088	0.86[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2403104	0.81[JPT][hapmap]
rs28377260	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28439950	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28564613	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28677919	0.84[AFR][1000 genomes]
rs2896452	0.90[JPT][hapmap]
rs2896453	0.81[ASN][1000 genomes]
rs2896454	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34103685	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3779899	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3779901	0.83[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3808538	0.86[JPT][hapmap]
rs3808539	0.82[JPT][hapmap]
rs4150859	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4150862	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4150865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150867	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150868	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150869	0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150884	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150897	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150909	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4150942	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150944	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4150962	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150964	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150974	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150977	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4609189	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4617148	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4739698	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4739700	0.86[JPT][hapmap]
rs4740043	0.82[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4740047	0.84[ASN][1000 genomes]
rs4740049	0.82[JPT][hapmap]
rs62527168	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62527173	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6605609	0.85[EUR][1000 genomes]
rs6605610	0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6605611	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6605624	0.90[JPT][hapmap]
rs6986704	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6990449	0.87[JPT][hapmap]
rs6993316	0.84[ASN][1000 genomes]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7001359	0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs7004765	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7011001	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7011926	0.82[JPT][hapmap]
rs7015758	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7818090	0.84[EUR][1000 genomes]
rs7818163	0.86[JPT][hapmap]
rs7821629	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7823218	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7826589	0.86[JPT][hapmap]
rs7827175	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7829050	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7829144	0.90[JPT][hapmap]
rs7829240	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7839129	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7841142	0.90[JPT][hapmap]
rs7842013	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903895	0.82[JPT][hapmap]
rs903896	0.82[JPT][hapmap]
rs903897	0.82[JPT][hapmap]
rs9329908	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2403086	LRRCC1	cis	normal skin	skin_eQTL
rs2403086	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2403086	LRRCC1	cis	Artery Tibial	GTEx
rs2403086	LRRCC1	cis	uninvolved skin	skin_eQTL
rs2403086	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs2403086	LRRCC1	cis	lesional skin	skin_eQTL
rs2403086	LRRCC1	cis	Esophagus Mucosa	GTEx
rs2403086	CA13	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 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	chr8:86096600-86120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:86100400-86121400	Weak transcription	Fetal Intestine Large	intestine
12	chr8:86101000-86122600	Weak transcription	Fetal Intestine Small	intestine
13	chr8:86101000-86124600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:86101000-86127800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:86101200-86127800	Weak transcription	Spleen	Spleen
16	chr8:86101200-86131000	Weak transcription	HepG2	liver
17	chr8:86102600-86113600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:86102600-86121000	Weak transcription	Fetal Muscle Leg	muscle
19	chr8:86102600-86121600	Weak transcription	Dnd41	blood
20	chr8:86102600-86125000	Weak transcription	Fetal Stomach	stomach
21	chr8:86102600-86125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:86102600-86128200	Weak transcription	Fetal Brain Male	brain
23	chr8:86103200-86118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:86103200-86120800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr8:86106000-86120800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr8:86108000-86114200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:86108200-86121400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:86110200-86114400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr8:86110400-86121000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr8:86110400-86128200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr8:86110600-86114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr8:86110600-86119200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:86110600-86126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr8:86111000-86121000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:86111000-86121000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr8:86111000-86128000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr8:86112000-86113400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:86112000-86113400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr8:86112400-86113400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:86112600-86113400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr8:86112800-86113400	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr8:86112800-86113400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr8:86112800-86113400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:86112800-86113400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr8:86112800-86113400	Enhancers	Colon Smooth Muscle	Colon
46	chr8:86112800-86113400	Enhancers	Osteobl	bone
47	chr8:86112800-86113800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr8:86112800-86113800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr8:86112800-86114400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:86112800-86114800	Flanking Active TSS	GM12878-XiMat	blood

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