Variant report

Variant	rs476138
Chromosome Location	chr6:13408402-13408403
allele	G/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	MAX	chr6:13408065-13408503	K562	blood:	n/a	n/a
2	FOXM1	chr6:13407790-13408632	ECC-1	luminal epithelium:	n/a	chr6:13408108-13408116
3	STAT5A	chr6:13407963-13408463	K562	blood:	n/a	n/a
4	MBD4	chr6:13407696-13408821	HepG2	liver:	n/a	n/a
5	CEBPB	chr6:13407700-13408626	MCF-7	breast:	n/a	chr6:13408161-13408172 chr6:13408508-13408519 chr6:13408163-13408174
6	MYC	chr6:13407795-13408525	NB4	blood:	n/a	n/a
7	FOXA1	chr6:13407716-13408424	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:13407841-13408543	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr6:13407786-13408529	HepG2	liver:	n/a	n/a
10	TEAD4	chr6:13407942-13408528	A549	lung:	n/a	n/a
11	FOXA2	chr6:13407908-13408441	A549	lung:	n/a	n/a
12	USF2	chr6:13407756-13408889	Hela-S3	cervix:	n/a	n/a
13	SMC3	chr6:13407910-13408420	HepG2	liver:	n/a	n/a
14	RCOR1	chr6:13407726-13408641	Hela-S3	cervix:	n/a	n/a
15	GATA3	chr6:13407683-13408485	A549	lung:	n/a	chr6:13407871-13407880 chr6:13407868-13407878 chr6:13408466-13408476
16	MBD4	chr6:13407821-13408474	HepG2	liver:	n/a	n/a
17	UBTF	chr6:13408129-13408609	K562	blood:	n/a	n/a
18	TBP	chr6:13407817-13408527	Hela-S3	cervix:	n/a	n/a
19	MAZ	chr6:13407962-13408488	Hela-S3	cervix:	n/a	n/a
20	NR2F2	chr6:13407948-13408516	K562	blood:	n/a	n/a
21	GATA3	chr6:13407501-13408684	MCF-7	breast:	n/a	chr6:13408545-13408552 chr6:13407871-13407880 chr6:13407868-13407878 chr6:13408466-13408476
22	STAT3	chr6:13407880-13408455	MCF10A-Er-Src	breast:	n/a	n/a
23	HDAC2	chr6:13408063-13408402	K562	blood:	n/a	n/a
24	MAX	chr6:13407618-13408541	Hela-S3	cervix:	n/a	n/a
25	TEAD4	chr6:13407936-13408558	K562	blood:	n/a	n/a
26	JUND	chr6:13407942-13408613	K562	blood:	n/a	chr6:13408104-13408114 chr6:13408461-13408470
27	EP300	chr6:13407518-13408544	HepG2	liver:	n/a	n/a
28	NR2F2	chr6:13407702-13408702	K562	blood:	n/a	n/a
29	MAX	chr6:13407873-13408514	A549	lung:	n/a	n/a
30	SIN3AK20	chr6:13407688-13408544	MCF-7	breast:	n/a	n/a
31	GATA3	chr6:13407538-13408620	A549	lung:	n/a	chr6:13408545-13408552 chr6:13407871-13407880 chr6:13407868-13407878 chr6:13408466-13408476
32	BCL3	chr6:13407695-13408474	A549	lung:	n/a	n/a
33	RAD21	chr6:13407760-13408415	HepG2	liver:	n/a	n/a
34	CEBPB	chr6:13407868-13408467	A549	lung:	n/a	chr6:13408161-13408172 chr6:13408163-13408174
35	CBX3	chr6:13407611-13408458	K562	blood:	n/a	n/a
36	NR3C1	chr6:13407793-13408491	A549	lung:	n/a	n/a
37	TAL1	chr6:13408023-13408430	K562	blood:	n/a	n/a
38	FOS	chr6:13407921-13408420	MCF10A-Er-Src	breast:	n/a	chr6:13408104-13408114
39	FOS	chr6:13407789-13408481	MCF10A-Er-Src	breast:	n/a	chr6:13408104-13408114 chr6:13408461-13408470
40	MAX	chr6:13407833-13408469	A549	lung:	n/a	n/a
41	TEAD4	chr6:13407650-13408670	K562	blood:	n/a	n/a
42	CEBPB	chr6:13407847-13408462	K562	blood:	n/a	chr6:13408161-13408172 chr6:13408163-13408174
43	STAT3	chr6:13407867-13408418	MCF10A-Er-Src	breast:	n/a	n/a
44	MAX	chr6:13407904-13408812	ECC-1	luminal epithelium:	n/a	n/a
45	RFX5	chr6:13407699-13408490	Hela-S3	cervix:	n/a	n/a
46	GATA3	chr6:13407655-13408479	MCF-7	breast:	n/a	chr6:13407871-13407880 chr6:13407868-13407878 chr6:13408466-13408476
47	CEBPB	chr6:13407835-13408471	ECC-1	luminal epithelium:	n/a	chr6:13408161-13408172 chr6:13408163-13408174
48	NFIC	chr6:13407543-13408676	HepG2	liver:	n/a	n/a
49	RCOR1	chr6:13407890-13408530	HepG2	liver:	n/a	n/a
50	TBL1XR1	chr6:13408099-13408546	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13404530..13406535-chr6:13408392..13410401,3	K562	blood:
2	chr6:13408139..13410381-chr6:13486541..13489029,3	MCF-7	breast:
3	chr6:13408206..13410464-chr6:13614798..13617307,2	MCF-7	breast:
4	chr6:13406818..13408886-chr6:13483840..13488220,5	MCF-7	breast:
5	chr6:13406137..13408577-chr6:13573927..13576170,2	MCF-7	breast:

Variant related genes	Relation type
GFOD1	TF binding region
ENSG00000225921	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000187461	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1345031	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345032	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550520	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1550521	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119481	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119484	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165419	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4454121	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715251	0.94[ASN][1000 genomes]
rs4715261	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485804	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs488885	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490443	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494026	0.87[ASN][1000 genomes]
rs500197	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs500293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503117	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513613	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519657	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519890	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520828	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs536916	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536998	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544639	0.82[EUR][1000 genomes]
rs546507	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550403	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559565	0.92[ASN][1000 genomes]
rs559612	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563424	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563662	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564361	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566320	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62386724	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6458814	0.83[EUR][1000 genomes]
rs6458815	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6910652	0.83[EUR][1000 genomes]
rs7742086	0.87[ASN][1000 genomes]
rs821298	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821299	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs821300	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370104	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9395768	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9474117	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13403600-13409600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:13404000-13408800	Enhancers	Brain Angular Gyrus	brain
4	chr6:13404000-13409000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:13404400-13408800	Enhancers	Adipose Nuclei	Adipose
6	chr6:13404400-13408800	Enhancers	Left Ventricle	heart
7	chr6:13404400-13408800	Enhancers	Psoas Muscle	Psoas
8	chr6:13404400-13408800	Enhancers	Right Atrium	heart
9	chr6:13404400-13409000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:13404400-13411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:13404800-13408600	Enhancers	Spleen	Spleen
12	chr6:13405000-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:13405200-13408800	Enhancers	Brain Anterior Caudate	brain
16	chr6:13405400-13409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:13405400-13410400	Weak transcription	Aorta	Aorta
18	chr6:13405600-13408600	Enhancers	Fetal Muscle Leg	muscle
19	chr6:13406000-13408600	Enhancers	Duodenum Mucosa	Duodenum
20	chr6:13406000-13408800	Enhancers	Primary B cells from cord blood	blood
21	chr6:13406000-13408800	Enhancers	Lung	lung
22	chr6:13406000-13408800	Enhancers	Right Ventricle	heart
23	chr6:13406200-13409000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:13406400-13408800	Flanking Active TSS	HepG2	liver
25	chr6:13406600-13408600	Enhancers	Colon Smooth Muscle	Colon
26	chr6:13406600-13408800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:13406600-13409000	Enhancers	Esophagus	oesophagus
28	chr6:13406800-13408800	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:13406800-13409000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:13406800-13409000	Enhancers	HMEC	breast
31	chr6:13407000-13408600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:13407000-13408600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:13407000-13408600	Enhancers	Fetal Lung	lung
34	chr6:13407000-13408600	Enhancers	Gastric	stomach
35	chr6:13407000-13408600	Enhancers	Pancreas	Pancrea
36	chr6:13407000-13408800	Strong transcription	GM12878-XiMat	blood
37	chr6:13407200-13408600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:13407200-13408600	Enhancers	Osteobl	bone
39	chr6:13407200-13408800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:13407200-13408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:13407200-13408800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:13407400-13408600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:13407400-13408600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:13407400-13408600	Enhancers	Placenta	Placenta
45	chr6:13407400-13408800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:13407400-13408800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:13407400-13408800	Enhancers	Stomach Mucosa	stomach
48	chr6:13407600-13408600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr6:13407600-13408600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr6:13407600-13408600	Flanking Active TSS	K562	blood

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