Variant report

Variant	rs7771980
Chromosome Location	chr6:45389289-45389290
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	CTCF	chr6:45389180-45389330	NB4	blood:	n/a	n/a
2	GTF2F1	chr6:45389137-45389753	Hela-S3	cervix:	n/a	n/a
3	EP300	chr6:45389200-45391505	SK-N-SH	brain:	n/a	n/a
4	MAZ	chr6:45389117-45390768	Hela-S3	cervix:	n/a	chr6:45389137-45389147
5	MAX	chr6:45389287-45390097	K562	blood:	n/a	n/a
6	RAD21	chr6:45389183-45389768	HCT-116	colon:	n/a	n/a
7	POLR2A	chr6:45389151-45389446	U87	brain:	n/a	n/a
8	MAX	chr6:45389245-45390616	A549	lung:	n/a	n/a
9	RAD21	chr6:45388419-45392074	IMR90	lung:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591 chr6:45388466-45388478
10	POLR2A	chr6:45389182-45392710	HL-60	blood:	n/a	n/a
11	MAX	chr6:45389076-45389699	SK-N-SH	brain:	n/a	chr6:45389137-45389147
12	RAD21	chr6:45389242-45390204	MCF-7	breast:	n/a	n/a
13	MAX	chr6:45389170-45390213	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:45389134-45390316	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:45389166-45392571	HL-60	blood:	n/a	n/a
16	CHD1	chr6:45388363-45391883	IMR90	lung:	n/a	chr6:45391066-45391076 chr6:45391635-45391645
17	MAFK	chr6:45389190-45389579	Hela-S3	cervix:	n/a	n/a
18	SMC3	chr6:45389042-45390791	Hela-S3	cervix:	n/a	n/a
19	SIN3A	chr6:45389123-45390301	H1-hESC	embryonic stem cell:	n/a	n/a
20	TBL1XR1	chr6:45389277-45389383	K562	blood:	n/a	n/a
21	RFX5	chr6:45389275-45390165	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr6:45389240-45389390	HAc	cerebellar:	n/a	n/a
23	TAF1	chr6:45389246-45389570	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr6:45389268-45390185	ECC-1	luminal epithelium:	n/a	n/a
25	CHD2	chr6:45389267-45390419	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr6:45389273-45390141	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr6:45389280-45389550	WI-38	lung:	n/a	n/a
28	TCF7L2	chr6:45389274-45390267	Hela-S3	cervix:	n/a	n/a
29	MAX	chr6:45389286-45390079	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr6:45388973-45389841	H1-neurons	neurons:	n/a	n/a
31	RAD21	chr6:45389259-45390129	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZBTB7A	chr6:45389160-45389703	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr6:45389255-45390289	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:45389260-45389798	Hela-S3	cervix:	n/a	n/a
35	MAX	chr6:45389267-45390190	SK-N-SH	brain:	n/a	n/a
36	CTBP2	chr6:45389219-45389758	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:45389256-45390144	MCF-7	breast:	n/a	n/a
38	MXI1	chr6:45389223-45392118	IMR90	lung:	n/a	n/a
39	POLR2A	chr6:45389249-45389408	SK-N-SH	brain:	n/a	n/a
40	TEAD4	chr6:45389222-45390074	K562	blood:	n/a	n/a
41	RAD21	chr6:45389075-45390508	HCT-116	colon:	n/a	n/a
42	POLR2A	chr6:45389241-45392606	NB4	blood:	n/a	n/a
43	EBF1	chr6:45389071-45389370	GM12878	blood:	n/a	chr6:45389199-45389212 chr6:45389201-45389210 chr6:45389200-45389211 chr6:45389201-45389210 chr6:45389200-45389210
44	POLR2A	chr6:45388936-45390689	H1-neurons	neurons:	n/a	n/a
45	ZBTB7A	chr6:45389125-45389721	ECC-1	luminal epithelium:	n/a	n/a
46	MAZ	chr6:45389116-45390826	K562	blood:	n/a	chr6:45389137-45389147
47	ZNF143	chr6:45389272-45389789	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAX	chr6:45389248-45390024	A549	lung:	n/a	n/a
49	RAD21	chr6:45389238-45390285	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:45389150-45390255	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:45388588..45389630-chr6:45682064..45682718,3	MCF-7	breast:
2	chr6:45343194..45347445-chr6:45386856..45389425,4	MCF-7	breast:
3	chr6:45387795..45389727-chr6:45621998..45623537,2	MCF-7	breast:
4	chr6:45343131..45346998-chr6:45386286..45389886,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUPT3H-2	chr6:45388816-45389742	ENSG00000271857.1

Variant related genes	Relation type
RUNX2	TF binding region
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498760	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11498195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963804	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11966462	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11968177	0.80[ASN][1000 genomes]
rs17209846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17209853	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17209874	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17209881	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288355	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288376	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288390	0.83[ASN][1000 genomes]
rs17288397	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977152	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805811	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805818	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828722	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413613	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56789892	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57013196	0.80[ASN][1000 genomes]
rs58571027	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59397804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61467394	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6921145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751427	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7768466	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768666	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3495915	chr6:45388574-45392472	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3495916	chr6:45388574-45392472	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:45387000-45389400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr6:45387000-45389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
6	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:45387200-45389400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:45387200-45389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
11	chr6:45387200-45390800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr6:45387400-45389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:45387400-45389600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:45387400-45391000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr6:45387600-45389600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
16	chr6:45387800-45389400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:45387800-45389400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
18	chr6:45387800-45389400	Bivalent Enhancer	HUVEC	blood vessel
19	chr6:45387800-45389600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr6:45387800-45390000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr6:45388200-45389400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:45388200-45389400	Bivalent/Poised TSS	Aorta	Aorta
23	chr6:45388200-45389400	Weak transcription	Gastric	stomach
24	chr6:45388200-45389400	Weak transcription	Pancreas	Pancrea
25	chr6:45388200-45389400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
26	chr6:45388200-45389600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:45388200-45390800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
28	chr6:45388200-45391800	Active TSS	Ovary	ovary
29	chr6:45388200-45392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:45388200-45392000	Active TSS	NHDF-Ad	bronchial
31	chr6:45388200-45392400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:45388400-45389400	Bivalent/Poised TSS	A549	lung
33	chr6:45388400-45389400	Flanking Active TSS	Hela-S3	cervix
34	chr6:45388400-45389600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:45388400-45393400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:45388600-45389600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:45388600-45390000	Active TSS	Right Ventricle	heart
38	chr6:45388600-45390200	Active TSS	Right Atrium	heart
39	chr6:45388600-45390800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:45388600-45390800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr6:45388600-45390800	Active TSS	Small Intestine	intestine
42	chr6:45388600-45391000	Active TSS	Brain Angular Gyrus	brain
43	chr6:45388600-45391600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:45388600-45391800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:45388600-45392000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr6:45388600-45392200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:45388600-45392800	Active TSS	HSMM	muscle
48	chr6:45388600-45393000	Active TSS	NHLF	lung
49	chr6:45388800-45389400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr6:45388800-45389400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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