Variant report

Variant	rs6909321
Chromosome Location	chr6:31093190-31093191
allele	A/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	FOS	chr6:31093049-31094144	MCF10A-Er-Src	breast:	n/a	chr6:31093229-31093240 chr6:31093888-31093895
2	TCF12	chr6:31092724-31093837	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr6:31092896-31093362	ECC-1	luminal epithelium:	n/a	n/a
4	EGR1	chr6:31092861-31093360	ECC-1	luminal epithelium:	n/a	chr6:31093093-31093102 chr6:31093093-31093104 chr6:31093093-31093103 chr6:31093092-31093105 chr6:31093091-31093105 chr6:31093093-31093103 chr6:31093093-31093104
5	POLR2A	chr6:31092991-31093274	HCT-116	colon:	n/a	n/a
6	FOS	chr6:31093051-31093394	MCF10A-Er-Src	breast:	n/a	chr6:31093229-31093240
7	POLR2A	chr6:31092952-31093265	HUVEC	blood vessel:	n/a	n/a
8	EP300	chr6:31092682-31093628	ECC-1	luminal epithelium:	n/a	chr6:31092920-31092934
9	POLR2A	chr6:31092976-31093338	HCT-116	colon:	n/a	n/a
10	FOS	chr6:31093047-31093408	MCF10A-Er-Src	breast:	n/a	chr6:31093229-31093240
11	EGR1	chr6:31092756-31093420	ECC-1	luminal epithelium:	n/a	chr6:31093093-31093102 chr6:31093093-31093104 chr6:31093093-31093103 chr6:31093092-31093105 chr6:31093091-31093105 chr6:31093093-31093103 chr6:31093093-31093104
12	TCF12	chr6:31092718-31093551	ECC-1	luminal epithelium:	n/a	n/a
13	FOS	chr6:31092988-31093418	MCF10A-Er-Src	breast:	n/a	chr6:31093229-31093240
14	MYC	chr6:31092985-31094184	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr6:31092937-31093486	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr6:31093090-31093341	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr6:31093038-31093377	HUVEC	blood vessel:	n/a	chr6:31093229-31093240
18	FOSL2	chr6:31093060-31093340	HepG2	liver:	n/a	n/a
19	EP300	chr6:31092819-31093387	ECC-1	luminal epithelium:	n/a	chr6:31092920-31092934
20	MYC	chr6:31093071-31093326	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr6:31093046-31093309	MCF10A-Er-Src	breast:	n/a	n/a
22	FOSL2	chr6:31092987-31093478	MCF-7	breast:	n/a	n/a
23	MYC	chr6:31093092-31093251	HUVEC	blood vessel:	n/a	n/a
24	STAT3	chr6:31092972-31093324	MCF10A-Er-Src	breast:	n/a	n/a
25	NFIC	chr6:31092778-31093890	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr6:31092807-31093503	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr6:31092701-31093219	ECC-1	luminal epithelium:	n/a	n/a
28	EGR1	chr6:31092833-31093422	HCT-116	colon:	n/a	chr6:31093093-31093102 chr6:31093093-31093104 chr6:31093093-31093103 chr6:31093092-31093105 chr6:31093091-31093105 chr6:31093093-31093103 chr6:31093093-31093104

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31093165-31093215	HepG2	liver:	n/a
2	chr6:31093153-31093203	PFSK-1	brain:	n/a
3	chr6:31093165-31093215	HRPEpiC	eye:	n/a
4	chr6:31093165-31093215	HCF	heart:	n/a
5	chr6:31093165-31093215	BJ	skin:	n/a
6	chr6:31093165-31093215	BE2_C	brain:	n/a
7	chr6:31093153-31093203	GM12892	blood:	n/a
8	chr6:31093165-31093215	NT2-D1	testis:	n/a
9	chr6:31093165-31093215	Hela-S3	cervix:	n/a
10	chr6:31093165-31093215	AG10803	skin:	n/a
11	chr6:31093165-31093215	U87	brain:	n/a
12	chr6:31093153-31093203	NH-A	brain:	n/a
13	chr6:31093153-31093203	HCT-116	colon:	n/a
14	chr6:31093153-31093203	HUVEC	blood vessel:	n/a
15	chr6:31093165-31093215	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:31093165-31093215	AG04449	skin:	fetal
17	chr6:31093165-31093215	H1-hESC	embryonic stem cell:	embryo
18	chr6:31093165-31093215	ovcar-3	ovarian:	n/a
19	chr6:31093165-31093215	HRE	kidney:	n/a
20	chr6:31093165-31093215	PrEC	prostate:	n/a
21	chr6:31093165-31093215	SK-N-SH_RA	brain:	n/a
22	chr6:31093153-31093203	AG09309	skin:	n/a
23	chr6:31093153-31093203	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:31093165-31093215	HCM	heart:	n/a
25	chr6:31093153-31093203	CMK	blood:	n/a
26	chr6:31093153-31093203	HAEpiC	amniotic membrane:	n/a
27	chr6:31093165-31093215	GM06990	blood:	n/a
28	chr6:31093165-31093215	HAEpiC	amniotic membrane:	n/a
29	chr6:31093153-31093203	A549	lung:	n/a
30	chr6:31093153-31093203	T-47D	breast:	n/a
31	chr6:31093165-31093215	HCT-116	colon:	n/a
32	chr6:31093153-31093203	Jurkat	blood:	n/a
33	chr6:31093165-31093215	GM12878	blood:	n/a
34	chr6:31093165-31093215	GM12892	blood:	n/a
35	chr6:31093165-31093215	T-47D	breast:	n/a
36	chr6:31093153-31093203	HL-60	blood:	n/a
37	chr6:31093165-31093215	HNPCEpiC	eye:	n/a
38	chr6:31093153-31093203	SKMC	muscle:	n/a
39	chr6:31093165-31093215	HIPEpiC	eye:	n/a
40	chr6:31093165-31093215	K562	blood:	n/a
41	chr6:31093153-31093203	SK-N-SH	brain:	n/a
42	chr6:31093153-31093203	SAEC	small airway:	n/a
43	chr6:31093165-31093215	HRCEpiC	kidney:	n/a
44	chr6:31093153-31093203	NT2-D1	testis:	n/a
45	chr6:31093153-31093203	PrEC	prostate:	n/a
46	chr6:31093165-31093215	NB4	blood:	n/a
47	chr6:31093165-31093215	NH-A	brain:	n/a
48	chr6:31093153-31093203	RPTEC	kidney:	n/a
49	chr6:31093153-31093203	MCF-7	breast:	n/a
50	chr6:31093153-31093203	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31081982..31084650-chr6:31092935..31096389,3	MCF-7	breast:
2	chr6:31091407..31094366-chr6:31165370..31167054,2	MCF-7	breast:
3	chr6:31088197..31091806-chr6:31092941..31094886,3	K562	blood:
4	chr6:31085584..31087243-chr6:31091042..31093736,2	K562	blood:
5	chr6:31092622..31094378-chr6:31124404..31127254,2	MCF-7	breast:
6	chr6:31090881..31093261-chr6:31094192..31096306,2	K562	blood:

Variant related genes	Relation type
CDSN	TF binding region
CDSN	CpG island
ENSG00000204539	Chromatin interaction
ENSG00000272501	Chromatin interaction
ENSG00000206344	Chromatin interaction
ENSG00000137310	Chromatin interaction
ENSG00000204536	Chromatin interaction
ENSG00000204540	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12191286	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12195316	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197796	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12199460	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12201248	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12204500	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12214039	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13198298	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13201757	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13204986	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13212902	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17196961	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734852	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3778639	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3778640	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6929464	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6931921	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6932086	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7756290	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	esv1797052	chr6:31083813-31095816	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv1820685	chr6:31083813-31097453	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	esv1799829	chr6:31087133-31097183	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6909321	XXbac-BPG248L24.12	cis	Thyroid	GTEx
rs6909321	XXbac-BPG248L24.12	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31083200-31094200	Weak transcription	Aorta	Aorta
2	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
3	chr6:31083400-31093400	Weak transcription	HSMMtube	muscle
4	chr6:31083800-31093600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:31085600-31093200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:31088000-31094200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:31088000-31094800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:31088000-31095000	Enhancers	HMEC	breast
9	chr6:31088200-31095000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:31089000-31096200	Enhancers	Lung	lung
11	chr6:31089600-31093600	Enhancers	HUVEC	blood vessel
12	chr6:31089600-31094800	Enhancers	NHEK	skin
13	chr6:31090000-31095800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:31090600-31094400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:31091200-31093600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:31091200-31093800	Enhancers	Colon Smooth Muscle	Colon
17	chr6:31091200-31094400	Weak transcription	Colonic Mucosa	Colon
18	chr6:31091200-31094400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:31091200-31096000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr6:31091400-31093200	Weak transcription	NHDF-Ad	bronchial
21	chr6:31091400-31094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:31091400-31094200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:31091600-31094400	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:31091800-31093200	Weak transcription	Esophagus	oesophagus
25	chr6:31092200-31094000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr6:31092200-31094000	Enhancers	NH-A	brain
27	chr6:31092200-31095200	Enhancers	Fetal Muscle Leg	muscle
28	chr6:31092400-31094800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:31092600-31094200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:31092600-31096000	Enhancers	Stomach Mucosa	stomach
31	chr6:31092800-31093200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:31092800-31093200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:31092800-31093200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:31092800-31093200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr6:31092800-31093200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr6:31092800-31093200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:31092800-31093400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr6:31092800-31093400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:31092800-31093400	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:31092800-31093600	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:31092800-31093800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:31092800-31093800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:31092800-31094000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:31092800-31094000	Enhancers	Fetal Thymus	thymus
45	chr6:31092800-31094200	Enhancers	A549	lung
46	chr6:31092800-31094200	Enhancers	Hela-S3	cervix
47	chr6:31092800-31094400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:31092800-31094600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:31092800-31094600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:31092800-31094600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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