Variant report

Variant	rs4150869
Chromosome Location	chr8:86099701-86099702
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	TBL1XR1	chr8:86099513-86100016	GM12878	blood:	n/a	n/a
2	SPI1	chr8:86099378-86100207	GM12878	blood:	n/a	n/a
3	MEF2A	chr8:86099495-86100034	GM12878	blood:	n/a	n/a
4	RUNX3	chr8:86099498-86100159	GM12878	blood:	n/a	n/a
5	NFIC	chr8:86099404-86100119	GM12878	blood:	n/a	n/a
6	SPI1	chr8:86099655-86100031	GM12878	blood:	n/a	n/a
7	RUNX3	chr8:86099650-86100034	GM12878	blood:	n/a	n/a
8	SPI1	chr8:86099682-86099928	GM12878	blood:	n/a	n/a
9	POLR2A	chr8:86099617-86099792	MCF10A-Er-Src	breast:	n/a	n/a
10	BCLAF1	chr8:86099406-86099989	GM12878	blood:	n/a	n/a
11	SPI1	chr8:86099678-86100019	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86088862..86093405-chr8:86093868..86100908,10	K562	blood:
2	chr8:86089844..86092252-chr8:86098327..86100668,2	MCF-7	breast:

Variant related genes	Relation type
E2F5	TF binding region
ENSG00000133740	Chromatin interaction
ENSG00000260493	Chromatin interaction
ENSG00000254208	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10088120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10090196	0.85[JPT][hapmap]
rs10091577	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10091710	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10100442	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1021583	0.90[JPT][hapmap]
rs11261468	0.90[JPT][hapmap]
rs11261471	0.85[JPT][hapmap]
rs12541445	0.85[JPT][hapmap]
rs12543256	0.90[JPT][hapmap]
rs12544332	0.81[JPT][hapmap]
rs12546106	0.90[JPT][hapmap]
rs12549421	0.83[ASN][1000 genomes]
rs12550160	0.90[JPT][hapmap]
rs12926	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1303806	0.81[JPT][hapmap]
rs13249364	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13259399	0.85[JPT][hapmap]
rs13269031	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13269739	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1390711	0.81[JPT][hapmap]
rs1496531	0.80[JPT][hapmap]
rs1496532	0.80[JPT][hapmap]
rs1553015	0.80[JPT][hapmap]
rs16913600	0.81[CEU][hapmap]
rs16913681	0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16913721	0.85[JPT][hapmap]
rs17740658	0.90[JPT][hapmap]
rs1908762	0.84[JPT][hapmap]
rs1995057	0.85[JPT][hapmap]
rs1995058	0.80[JPT][hapmap]
rs2006767	0.85[JPT][hapmap]
rs2132589	0.90[JPT][hapmap]
rs2278459	0.90[JPT][hapmap]
rs2279701	0.85[JPT][hapmap]
rs2291786	0.90[JPT][hapmap]
rs2291787	0.85[JPT][hapmap]
rs2403082	0.85[EUR][1000 genomes]
rs2403083	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2403084	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2403085	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]
rs2403086	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]
rs2403088	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2403089	0.84[EUR][1000 genomes]
rs28377260	0.82[EUR][1000 genomes]
rs28621707	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2896452	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2896454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34103685	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs34527380	0.88[ASN][1000 genomes]
rs3779899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779901	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3808538	0.85[JPT][hapmap]
rs3808539	0.80[JPT][hapmap]
rs4150859	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150862	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4150865	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150884	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150893	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150909	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4150942	0.91[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs4150944	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4150962	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4150964	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4150974	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4150977	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4609189	0.90[JPT][hapmap]
rs4739700	0.85[JPT][hapmap]
rs4740043	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4740044	0.85[JPT][hapmap]
rs4740045	0.90[JPT][hapmap]
rs4740049	0.80[JPT][hapmap]
rs62527168	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62527173	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6605609	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6605610	0.90[JPT][hapmap]
rs6605611	0.89[JPT][hapmap]
rs6605624	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs6605625	0.84[EUR][1000 genomes]
rs6986704	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6990449	0.80[JPT][hapmap]
rs6993387	0.85[JPT][hapmap]
rs6994113	0.90[JPT][hapmap]
rs7001359	0.85[JPT][hapmap]
rs7004765	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7008032	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7008772	0.85[JPT][hapmap]
rs7010228	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7011926	0.80[JPT][hapmap]
rs7015758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7814435	0.86[AMR][1000 genomes]
rs7818090	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7818163	0.85[JPT][hapmap]
rs7823218	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.90[JPT][hapmap]
rs7829050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7829144	0.90[JPT][hapmap]
rs7838900	0.81[AMR][1000 genomes]
rs7841142	0.90[JPT][hapmap]
rs7842013	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903895	0.80[JPT][hapmap]
rs903896	0.80[JPT][hapmap]
rs903897	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1799571	chr8:86064130-86105803	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
4	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
5	esv3396459	chr8:86098050-86100248	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4150869	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs4150869	LRRCC1	cis	uninvolved skin	skin_eQTL
rs4150869	LRRCC1	cis	Artery Tibial	GTEx
rs4150869	LRRCC1	cis	lesional skin	skin_eQTL
rs4150869	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs4150869	LRRCC1	cis	normal skin	skin_eQTL
rs4150869	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86090800-86127800	Weak transcription	Aorta	Aorta
2	chr8:86091000-86101800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:86091000-86103600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:86091000-86127800	Weak transcription	HSMMtube	muscle
5	chr8:86091000-86132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:86091200-86125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:86091600-86100600	Weak transcription	Fetal Stomach	stomach
8	chr8:86091600-86101000	Weak transcription	Thymus	Thymus
9	chr8:86091600-86107600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:86091600-86107800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:86091600-86110000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:86091600-86124200	Weak transcription	Primary T cells from cord blood	blood
13	chr8:86091600-86126000	Weak transcription	Hela-S3	cervix
14	chr8:86091800-86100400	Weak transcription	Fetal Heart	heart
15	chr8:86091800-86100600	Weak transcription	Dnd41	blood
16	chr8:86091800-86124200	Weak transcription	HMEC	breast
17	chr8:86093600-86100600	Weak transcription	Fetal Thymus	thymus
18	chr8:86096200-86108400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:86096200-86121400	Weak transcription	Fetal Lung	lung
20	chr8:86096400-86100200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:86096400-86102000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr8:86096400-86107800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr8:86096400-86121400	Weak transcription	A549	lung
24	chr8:86096600-86101600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr8:86096600-86120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:86096800-86100000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr8:86096800-86100600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:86096800-86109600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr8:86096800-86113000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:86097000-86102400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:86098000-86101200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:86098000-86101600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr8:86098000-86112800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr8:86099400-86099800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr8:86099400-86100000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr8:86099400-86100200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr8:86099400-86100400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:86099400-86100600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr8:86099400-86100600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr8:86099400-86100600	Active TSS	GM12878-XiMat	blood
41	chr8:86099400-86101200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:86099400-86101400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr8:86099400-86102200	Weak transcription	Fetal Muscle Leg	muscle
44	chr8:86099600-86099800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr8:86099600-86100000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr8:86099600-86100400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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