Variant report

Variant	rs9493180
Chromosome Location	chr6:132453246-132453247
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	RAD21	chr6:132452589-132453406	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:132453003-132453291	HUVEC	blood vessel:	n/a	n/a
3	CEBPB	chr6:132452507-132453278	IMR90	lung:	n/a	n/a
4	MAX	chr6:132451961-132453420	SK-N-SH	brain:	n/a	chr6:132453025-132453034
5	TCF12	chr6:132452658-132453446	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr6:132451556-132457610	HUVEC	blood vessel:	n/a	n/a
7	STAT3	chr6:132452889-132453386	MCF10A-Er-Src	breast:	n/a	chr6:132453141-132453153
8	NFIC	chr6:132451996-132453377	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr6:132452678-132453392	A549	lung:	n/a	chr6:132453024-132453033
10	GATA2	chr6:132452850-132453315	HUVEC	blood vessel:	n/a	chr6:132453024-132453033
11	POLR2A	chr6:132452783-132453371	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr6:132451723-132457447	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr6:132452847-132453274	HUVEC	blood vessel:	n/a	n/a
14	SIN3AK20	chr6:132452810-132453298	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr6:132452025-132454614	SK-N-SH	brain:	n/a	chr6:132453521-132453529 chr6:132452653-132452663 chr6:132453717-132453727 chr6:132452653-132452660 chr6:132453024-132453033 chr6:132453519-132453532 chr6:132452651-132452660 chr6:132452651-132452661 chr6:132453729-132453742 chr6:132453560-132453576 chr6:132453567-132453574
16	PBX3	chr6:132452782-132453375	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr6:132452935-132453267	SK-N-SH_RA	brain:	n/a	n/a
18	FOSL2	chr6:132452830-132453312	A549	lung:	n/a	chr6:132453026-132453034 chr6:132453024-132453036 chr6:132453025-132453035 chr6:132453025-132453035
19	POLR2A	chr6:132452851-132453273	U87	brain:	n/a	n/a
20	MAZ	chr6:132452743-132454457	IMR90	lung:	n/a	chr6:132453025-132453034
21	REST	chr6:132452896-132453383	PFSK-1	brain:	n/a	n/a
22	FOXA1	chr6:132452891-132453345	HepG2	liver:	n/a	n/a
23	EP300	chr6:132452903-132453336	SK-N-SH_RA	brain:	n/a	n/a
24	SP1	chr6:132452881-132453326	A549	lung:	n/a	chr6:132453139-132453149 chr6:132453138-132453150 chr6:132453037-132453051 chr6:132453155-132453169 chr6:132453145-132453155
25	MAX	chr6:132452823-132453343	SK-N-SH	brain:	n/a	chr6:132453025-132453034
26	FOS	chr6:132452856-132453305	MCF10A-Er-Src	breast:	n/a	chr6:132453026-132453034 chr6:132453024-132453036 chr6:132453025-132453035 chr6:132453025-132453035 chr6:132453024-132453035
27	POLR2A	chr6:132452037-132454754	IMR90	lung:	n/a	n/a
28	MAFK	chr6:132452587-132453429	IMR90	lung:	n/a	n/a
29	FOS	chr6:132452810-132453348	HUVEC	blood vessel:	n/a	chr6:132453026-132453034 chr6:132453024-132453036 chr6:132453025-132453035 chr6:132453025-132453035 chr6:132453024-132453035
30	EP300	chr6:132452836-132453254	SK-N-SH_RA	brain:	n/a	chr6:132452897-132452911
31	EP300	chr6:132452674-132453382	SK-N-SH	brain:	n/a	chr6:132452897-132452911
32	POLR2A	chr6:132451762-132455651	HUVEC	blood vessel:	n/a	n/a
33	JUND	chr6:132452718-132453463	SK-N-SH	brain:	n/a	chr6:132452759-132452769 chr6:132453026-132453034 chr6:132452759-132452769 chr6:132453024-132453036 chr6:132452759-132452769 chr6:132453342-132453351 chr6:132453024-132453035 chr6:132453025-132453035 chr6:132453025-132453035
34	STAT3	chr6:132452915-132453258	MCF10A-Er-Src	breast:	n/a	chr6:132453141-132453153
35	RAD21	chr6:132452873-132453313	SK-N-SH_RA	brain:	n/a	n/a
36	STAT3	chr6:132452894-132453257	MCF10A-Er-Src	breast:	n/a	chr6:132453141-132453153
37	POLR2A	chr6:132452851-132453248	U87	brain:	n/a	n/a
38	JUN	chr6:132452759-132453398	HUVEC	blood vessel:	n/a	chr6:132452759-132452769 chr6:132453026-132453034 chr6:132452759-132452769 chr6:132453024-132453036 chr6:132452759-132452769 chr6:132453342-132453351 chr6:132453025-132453035 chr6:132453012-132453025 chr6:132453025-132453035
39	KAP1	chr6:132452533-132453472	U2OS	brain:	n/a	n/a
40	JUND	chr6:132452176-132453440	SK-N-SH	brain:	n/a	chr6:132452759-132452769 chr6:132453026-132453034 chr6:132452759-132452769 chr6:132453024-132453036 chr6:132452759-132452769 chr6:132453342-132453351 chr6:132453024-132453035 chr6:132453025-132453035 chr6:132453025-132453035
41	FOS	chr6:132452876-132453258	MCF10A-Er-Src	breast:	n/a	chr6:132453026-132453034 chr6:132453024-132453036 chr6:132453025-132453035 chr6:132453025-132453035 chr6:132453024-132453035
42	TCF12	chr6:132451772-132453534	SK-N-SH	brain:	n/a	n/a
43	PBX3	chr6:132452711-132453472	SK-N-SH	brain:	n/a	n/a
44	GATA3	chr6:132452599-132454487	SK-N-SH	brain:	n/a	chr6:132453521-132453529 chr6:132452653-132452663 chr6:132453717-132453727 chr6:132452653-132452660 chr6:132453024-132453033 chr6:132453519-132453532 chr6:132452651-132452660 chr6:132452651-132452661 chr6:132453729-132453742 chr6:132453560-132453576 chr6:132453567-132453574
45	FOSL2	chr6:132452700-132453523	SK-N-SH	brain:	n/a	chr6:132452759-132452769 chr6:132453026-132453034 chr6:132452759-132452769 chr6:132453024-132453036 chr6:132452759-132452769 chr6:132453342-132453351 chr6:132453025-132453035 chr6:132453025-132453035
46	FOSL2	chr6:132452649-132453303	SK-N-SH	brain:	n/a	chr6:132452759-132452769 chr6:132453026-132453034 chr6:132452759-132452769 chr6:132453024-132453036 chr6:132452759-132452769 chr6:132453025-132453035 chr6:132453025-132453035
47	FOXA2	chr6:132452801-132453260	A549	lung:	n/a	n/a
48	REST	chr6:132452896-132453264	SK-N-SH	brain:	n/a	n/a
49	FOXA2	chr6:132452936-132453308	A549	lung:	n/a	n/a
50	KAP1	chr6:132452615-132453480	HEK293	kidney:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOXD1-1	chr6:132452888-132453272	XLOC_005832
2	lnc-ENPP1-4	chr6:132453094-132453329	XLOC_005465
3	lnc-ENPP1-4	chr6:132453094-132453329	XLOC_005465

Variant related genes	Relation type
LINC01013	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11154664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1321265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1321266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1321267	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1321270	0.82[JPT][hapmap]
rs1569448	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1569450	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807983	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4305744	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4895928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4895929	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897559	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6900897	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6909982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9483385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483388	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9493185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9493186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762616	chr6:132404708-132584324	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132450400-132456600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:132451000-132455600	Enhancers	Fetal Stomach	stomach
3	chr6:132451200-132455000	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:132451200-132455400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:132451200-132455600	Enhancers	Fetal Muscle Leg	muscle
6	chr6:132451400-132453800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:132451400-132454400	Enhancers	Ovary	ovary
8	chr6:132451400-132454600	Enhancers	Rectal Smooth Muscle	rectum
9	chr6:132451400-132454800	Enhancers	Right Atrium	heart
10	chr6:132451400-132455400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:132451400-132455600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:132451400-132455600	Enhancers	NHLF	lung
13	chr6:132451400-132456000	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:132451600-132453400	Enhancers	Fetal Brain Male	brain
15	chr6:132451600-132454000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:132451600-132454200	Weak transcription	Aorta	Aorta
17	chr6:132451600-132454400	Enhancers	Fetal Heart	heart
18	chr6:132451600-132454600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:132451600-132455000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:132451600-132455000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr6:132451600-132455600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:132451600-132455600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:132451600-132455600	Enhancers	Adipose Nuclei	Adipose
24	chr6:132451800-132453600	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:132451800-132453800	Enhancers	Brain Germinal Matrix	brain
26	chr6:132451800-132454600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:132451800-132455200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:132451800-132455600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:132451800-132455600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:132452000-132453400	Enhancers	Fetal Lung	lung
31	chr6:132452000-132454000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr6:132452000-132454400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:132452000-132454400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:132452000-132454400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:132452000-132454600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:132452200-132453800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr6:132452200-132454000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr6:132452200-132454200	Enhancers	Stomach Mucosa	stomach
39	chr6:132452200-132454600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr6:132452200-132454600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr6:132452200-132454800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:132452200-132456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:132452400-132453800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:132452400-132454600	Enhancers	Fetal Intestine Small	intestine
45	chr6:132452400-132455000	Enhancers	Brain Angular Gyrus	brain
46	chr6:132452400-132455600	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:132452600-132454200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:132452600-132454600	Enhancers	Primary B cells from cord blood	blood
49	chr6:132452600-132454600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:132452600-132454600	Enhancers	HMEC	breast

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