Variant report

Variant	rs11261468
Chromosome Location	chr8:86018853-86018854
allele	C/T
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	RELA	chr8:86018831-86020095	GM10847	blood:	n/a	n/a
2	POLR2A	chr8:86018786-86020294	PBDE	blood:	n/a	n/a
3	RCOR1	chr8:86018806-86019546	GM12878	blood:	n/a	n/a
4	MAX	chr8:86018810-86020215	HCT-116	colon:	n/a	n/a
5	BATF	chr8:86018784-86019506	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:86018797-86019865	GM18526	blood:	n/a	n/a
7	POLR2A	chr8:86018685-86020125	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr8:86018622-86020478	SK-N-MC	brain:	n/a	n/a
9	TRIM28	chr8:86018770-86019552	K562	blood:	n/a	n/a
10	GABPA	chr8:86018807-86020052	MCF-7	breast:	n/a	n/a
11	EBF1	chr8:86018750-86019084	GM12878	blood:	n/a	n/a
12	IKZF1	chr8:86018825-86019380	GM12878	blood:	n/a	n/a
13	RELA	chr8:86018793-86020120	GM19099	blood:	n/a	n/a
14	WRNIP1	chr8:86018835-86019242	GM12878	blood:	n/a	n/a
15	RFX5	chr8:86018850-86019568	Hela-S3	cervix:	n/a	n/a
16	RUNX3	chr8:86018670-86019553	GM12878	blood:	n/a	n/a
17	GTF2B	chr8:86018836-86019482	K562	blood:	n/a	n/a
18	E2F6	chr8:86018837-86020006	K562	blood:	n/a	chr8:86019377-86019388 chr8:86019380-86019387 chr8:86019376-86019388 chr8:86019716-86019725 chr8:86019380-86019387 chr8:86019380-86019387 chr8:86019828-86019840
19	POLR2A	chr8:86018853-86019883	GM12878	blood:	n/a	n/a
20	SPI1	chr8:86018787-86019331	HL-60	blood:	n/a	n/a
21	REST	chr8:86018714-86020332	H1-neurons	neurons:	n/a	chr8:86020068-86020081
22	EP300	chr8:86018807-86019497	GM12878	blood:	n/a	n/a
23	MAX	chr8:86018812-86020127	HepG2	liver:	n/a	n/a
24	ATF2	chr8:86018816-86019640	GM12878	blood:	n/a	n/a
25	POLR2A	chr8:86018761-86020237	K562	blood:	n/a	n/a
26	SIN3AK20	chr8:86018744-86020228	MCF-7	breast:	n/a	n/a
27	MTA3	chr8:86018630-86020112	GM12878	blood:	n/a	n/a
28	RUNX3	chr8:86018773-86020077	GM12878	blood:	n/a	n/a
29	RCOR1	chr8:86018842-86019935	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86016436..86019868-chr8:86087554..86092567,7	K562	blood:

Variant related genes	Relation type
LRRCC1	TF binding region
ENSG00000133740	Chromatin interaction
ENSG00000260493	Chromatin interaction
ENSG00000254208	Chromatin interaction

Extended variants
information (count: 80 )
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];0.88[MEX][hapmap]
rs10090196	0.95[JPT][hapmap]
rs10100442	0.84[JPT][hapmap]
rs10104630	0.82[JPT][hapmap]
rs1021583	0.85[JPT][hapmap]
rs11261471	0.81[JPT][hapmap];0.80[MEX][hapmap]
rs12541445	0.81[JPT][hapmap];0.80[MEX][hapmap]
rs12543256	0.85[JPT][hapmap]
rs12546106	0.85[JPT][hapmap];0.84[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];0.91[MEX][hapmap]
rs16913600	0.86[TSI][hapmap]
rs16913681	0.85[JPT][hapmap]
rs16913721	0.95[JPT][hapmap];0.84[MEX][hapmap]
rs17740658	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs1851973	0.82[JPT][hapmap]
rs1908762	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs2006767	0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2132589	0.85[JPT][hapmap]
rs2278459	0.87[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs2279701	0.81[JPT][hapmap]
rs2291786	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs2403082	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2403083	0.90[JPT][hapmap]
rs2403085	0.91[JPT][hapmap]
rs2403086	0.90[JPT][hapmap]
rs2403087	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs2403089	0.84[AMR][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];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2896454	0.80[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs34103685	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs3779899	0.80[GIH][hapmap];0.90[JPT][hapmap];0.92[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];0.84[MEX][hapmap]
rs4150909	0.91[JPT][hapmap]
rs4150942	0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4150944	0.91[JPT][hapmap]
rs4150964	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs4150974	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs4150977	0.85[JPT][hapmap];0.84[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];0.84[MEX][hapmap]
rs6605609	0.92[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];0.96[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6605625	0.83[AMR][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];0.84[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	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7827175	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs7829050	0.91[JPT][hapmap]
rs7829144	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]
rs7838900	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7841142	1.00[ASW][hapmap];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];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9692962	0.82[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11261468	C8orf59	cis	cerebellum	SCAN
rs11261468	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs11261468	LRRCC1	cis	Esophagus Mucosa	GTEx
rs11261468	C8orf59	cis	parietal	SCAN
rs11261468	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs11261468	LRRCC1	cis	parietal	SCAN
rs11261468	LRRCC1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86018400-86019000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr8:86018400-86019200	Flanking Active TSS	Dnd41	blood
3	chr8:86018400-86020200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr8:86018600-86019000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr8:86018600-86019000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr8:86018600-86019000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr8:86018600-86019000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr8:86018600-86019000	Flanking Active TSS	Colon Smooth Muscle	Colon
9	chr8:86018600-86019000	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr8:86018600-86019000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr8:86018600-86019000	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr8:86018600-86019000	Flanking Active TSS	Fetal Stomach	stomach
13	chr8:86018600-86019000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr8:86018600-86019200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:86018600-86019200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr8:86018600-86019200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr8:86018600-86019200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr8:86018600-86019200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr8:86018600-86019200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:86018600-86019200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr8:86018600-86019200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:86018600-86019200	Active TSS	Brain Germinal Matrix	brain
23	chr8:86018600-86019200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr8:86018600-86019200	Flanking Active TSS	HUVEC	blood vessel
25	chr8:86018600-86019200	Flanking Active TSS	K562	blood
26	chr8:86018600-86019200	Flanking Active TSS	NHEK	skin
27	chr8:86018600-86019200	Flanking Active TSS	Osteobl	bone
28	chr8:86018600-86019600	Active TSS	Primary T cells fromperipheralblood	blood
29	chr8:86018600-86019800	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr8:86018600-86019800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr8:86018600-86019800	Active TSS	Fetal Thymus	thymus
32	chr8:86018600-86020000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr8:86018600-86020000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr8:86018600-86020000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr8:86018600-86020000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:86018600-86020000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:86018600-86020000	Active TSS	Brain Cingulate Gyrus	brain
38	chr8:86018600-86020000	Active TSS	NHLF	lung
39	chr8:86018600-86020200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:86018600-86020200	Active TSS	Brain Angular Gyrus	brain
41	chr8:86018600-86020200	Active TSS	Fetal Intestine Large	intestine
42	chr8:86018600-86020200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr8:86018600-86020200	Active TSS	Right Atrium	heart
44	chr8:86018600-86020200	Active TSS	Right Ventricle	heart
45	chr8:86018600-86020200	Active TSS	NHDF-Ad	bronchial
46	chr8:86018600-86020400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr8:86018600-86020400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr8:86018600-86020400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:86018600-86020400	Active TSS	Colonic Mucosa	Colon
50	chr8:86018600-86020400	Active TSS	Fetal Brain Male	brain

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