Variant report

Variant	rs3800319
Chromosome Location	chr6:27280407-27280408
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:27280334-27280955	MCF-7	breast:	n/a	chr6:27280634-27280653
2	CTCF	chr6:27280360-27280510	GM12870	blood:	n/a	n/a
3	SIN3AK20	chr6:27280361-27280845	PANC-1	pancreas:	n/a	n/a
4	MTA3	chr6:27280186-27280822	GM12878	blood:	n/a	n/a
5	SMC3	chr6:27280398-27280911	HepG2	liver:	n/a	chr6:27280635-27280649
6	RAD21	chr6:27280119-27280965	ECC-1	luminal epithelium:	n/a	chr6:27280634-27280653
7	ZEB1	chr6:27280368-27280782	GM12878	blood:	n/a	n/a
8	MXI1	chr6:27280215-27280622	GM12878	blood:	n/a	n/a
9	MAX	chr6:27279479-27280881	A549	lung:	n/a	n/a
10	SMC3	chr6:27279813-27280962	SK-N-SH	brain:	n/a	chr6:27280635-27280649
11	YY1	chr6:27280349-27280886	HepG2	liver:	n/a	n/a
12	CTCF	chr6:27280332-27280889	H1-hESC	embryonic stem cell:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
13	RCOR1	chr6:27280395-27280807	HepG2	liver:	n/a	n/a
14	ELF1	chr6:27280283-27280977	MCF-7	breast:	n/a	chr6:27280597-27280608
15	RAD21	chr6:27280048-27280854	IMR90	lung:	n/a	chr6:27280634-27280653
16	RAD21	chr6:27280285-27280996	MCF-7	breast:	n/a	chr6:27280634-27280653
17	ELF1	chr6:27279673-27280871	GM12878	blood:	n/a	chr6:27280597-27280608
18	RAD21	chr6:27280404-27280847	SK-N-SH_RA	brain:	n/a	chr6:27280634-27280653
19	E2F6	chr6:27280156-27280435	A549	lung:	n/a	n/a
20	RUNX3	chr6:27280036-27280795	GM12878	blood:	n/a	n/a
21	ZNF143	chr6:27280381-27280835	H1-hESC	embryonic stem cell:	n/a	n/a
22	NRF1	chr6:27280262-27280895	GM12878	blood:	n/a	n/a
23	SMC3	chr6:27280089-27280913	GM12878	blood:	n/a	chr6:27280635-27280649
24	TCF12	chr6:27280379-27280792	H1-hESC	embryonic stem cell:	n/a	n/a
25	RCOR1	chr6:27280040-27280866	GM12878	blood:	n/a	n/a
26	CTCF	chr6:27280084-27280426	GM19239	blood:	n/a	n/a
27	RAD21	chr6:27280403-27280873	HepG2	liver:	n/a	chr6:27280634-27280653
28	REST	chr6:27280360-27280975	H1-neurons	neurons:	n/a	n/a
29	CTCF	chr6:27280036-27280912	GM12878	blood:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
30	MAX	chr6:27280319-27280915	MCF-7	breast:	n/a	n/a
31	E2F6	chr6:27279351-27280833	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr6:27280301-27280938	A549	lung:	n/a	chr6:27280634-27280653
33	PML	chr6:27280386-27280852	GM12878	blood:	n/a	n/a
34	BCLAF1	chr6:27280335-27280949	GM12878	blood:	n/a	n/a
35	RAD21	chr6:27279554-27280893	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
36	EBF1	chr6:27280389-27280747	GM12878	blood:	n/a	n/a
37	CTCF	chr6:27280320-27280470	MCF-7	breast:	n/a	n/a
38	STAT3	chr6:27280383-27280612	MCF10A-Er-Src	breast:	n/a	n/a
39	ZNF263	chr6:27280134-27280886	HEK293-T-REx	kidney:	n/a	n/a
40	PAX5	chr6:27280238-27280523	GM12892	blood:	n/a	n/a
41	SIN3A	chr6:27279775-27280838	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELF1	chr6:27280388-27280835	A549	lung:	n/a	chr6:27280597-27280608
43	RAD21	chr6:27280366-27280835	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
44	CTCF	chr6:27280093-27280836	IMR90	lung:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
45	CTCF	chr6:27280399-27280812	GM19240	blood:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
46	E2F6	chr6:27279160-27280852	H1-hESC	embryonic stem cell:	n/a	n/a
47	EBF1	chr6:27280310-27280745	GM12878	blood:	n/a	n/a
48	ELF1	chr6:27280053-27280836	GM12878	blood:	n/a	chr6:27280597-27280608
49	CHD2	chr6:27279689-27280725	H1-hESC	embryonic stem cell:	n/a	chr6:27280236-27280246 chr6:27280271-27280281
50	TCF12	chr6:27280217-27280899	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27280373-27280423	H1-hESC	embryonic stem cell:	embryo
2	chr6:27280373-27280423	HAEpiC	amniotic membrane:	n/a
3	chr6:27280373-27280423	IMR90	lung:	fetal
4	chr6:27280373-27280423	HUVEC	blood vessel:	n/a
5	chr6:27280373-27280423	GM06990	blood:	n/a
6	chr6:27280373-27280423	GM12878	blood:	n/a
7	chr6:27280373-27280423	MCF-7	breast:	n/a
8	chr6:27280373-27280423	ovcar-3	ovarian:	n/a
9	chr6:27280373-27280423	Hela-S3	cervix:	n/a
10	chr6:27280373-27280423	T-47D	breast:	n/a
11	chr6:27280373-27280423	HIPEpiC	eye:	n/a
12	chr6:27280373-27280423	U87	brain:	n/a
13	chr6:27280373-27280423	HepG2	liver:	n/a
14	chr6:27280373-27280423	AG10803	skin:	n/a
15	chr6:27280373-27280423	BJ	skin:	n/a
16	chr6:27280373-27280423	BE2_C	brain:	n/a
17	chr6:27280373-27280423	ECC-1	luminal epithelium:	n/a
18	chr6:27280373-27280423	HCM	heart:	n/a
19	chr6:27280373-27280423	HNPCEpiC	eye:	n/a
20	chr6:27280373-27280423	SK-N-SH	brain:	n/a
21	chr6:27280373-27280423	GM19239	blood:	n/a
22	chr6:27280373-27280423	HMEC	breast:	n/a
23	chr6:27280373-27280423	HRCEpiC	kidney:	n/a
24	chr6:27280373-27280423	Hepatocyte	liver:	n/a
25	chr6:27280373-27280423	SAEC	small airway:	n/a
26	chr6:27280373-27280423	NB4	blood:	n/a
27	chr6:27280373-27280423	NH-A	brain:	n/a
28	chr6:27280373-27280423	SKMC	muscle:	n/a
29	chr6:27280373-27280423	HCT-116	colon:	n/a
30	chr6:27280373-27280423	NT2-D1	testis:	n/a
31	chr6:27280373-27280423	NHBE	bronchial:	n/a
32	chr6:27280373-27280423	Caco-2	colon:	n/a
33	chr6:27280373-27280423	AG09309	skin:	n/a
34	chr6:27280373-27280423	ProgFib	skin:	n/a
35	chr6:27280373-27280423	Jurkat	blood:	n/a
36	chr6:27280373-27280423	PrEC	prostate:	n/a
37	chr6:27280373-27280423	LNCaP	prostate:	n/a
38	chr6:27280373-27280423	AoSMC	blood vessel:	n/a
39	chr6:27280373-27280423	AG04449	skin:	fetal
40	chr6:27280373-27280423	HRE	kidney:	n/a
41	chr6:27280373-27280423	HEEpiC	esophagus:	n/a
42	chr6:27280373-27280423	HEK293	kidney:	embryo
43	chr6:27280373-27280423	MCF10A-Er-Src	breast:	n/a
44	chr6:27280373-27280423	AG09319	gingival:	n/a
45	chr6:27280373-27280423	NHDF-neo	bronchial:	n/a
46	chr6:27280373-27280423	CMK	blood:	n/a
47	chr6:27280373-27280423	HRPEpiC	eye:	n/a
48	chr6:27280373-27280423	SK-N-SH_RA	brain:	n/a
49	chr6:27280373-27280423	K562	blood:	n/a
50	chr6:27280373-27280423	HPAEpiC	pulmonary alveolar:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27279187..27280995-chr6:27439360..27441808,2	MCF-7	breast:
2	chr6:27114741..27116846-chr6:27278241..27280578,2	K562	blood:
3	chr6:27280335..27283011-chr6:27292973..27294490,2	K562	blood:

No data

Variant related genes	Relation type
POM121L2	TF binding region
POM121L2	CpG island
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2092114	0.88[EUR][1000 genomes]
rs2295603	0.81[CEU][hapmap]
rs2893911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546474	0.81[CEU][hapmap]
rs4559087	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7744605	0.87[EUR][1000 genomes]
rs7746841	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs7771953	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368501	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9379968	0.89[CEU][hapmap]
rs9379971	1.00[JPT][hapmap]
rs9379973	0.81[EUR][1000 genomes]

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv883506	chr6:27271343-27288687	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3800319	ZNF391	cis	Artery Tibial	GTEx
rs3800319	AL022393.7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27279400-27280600	Active TSS	Gastric	stomach
2	chr6:27279400-27281000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27279600-27280600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr6:27279600-27280600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:27279600-27280800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:27279600-27280800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:27279600-27280800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:27279600-27281000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:27279600-27281000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:27279600-27281000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:27279800-27280600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:27279800-27280600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:27279800-27280600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
21	chr6:27279800-27280600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
23	chr6:27279800-27280800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
26	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:27279800-27280800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
28	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr6:27279800-27280800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr6:27279800-27280800	Active TSS	A549	lung
33	chr6:27279800-27280800	Bivalent/Poised TSS	HSMM	muscle
34	chr6:27279800-27281000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:27279800-27281000	Flanking Active TSS	HMEC	breast
36	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:27280000-27280600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
38	chr6:27280000-27280600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
40	chr6:27280000-27280600	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
41	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:27280000-27280600	Flanking Active TSS	Liver	Liver
45	chr6:27280000-27280600	Bivalent/Poised TSS	Fetal Kidney	kidney
46	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Placenta	Placenta
48	chr6:27280000-27280600	Flanking Active TSS	Lung	lung
49	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Right Ventricle	heart
50	chr6:27280000-27280600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

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