Variant report

Variant	rs6949538
Chromosome Location	chr7:79081703-79081704
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	RAD21	chr7:79081267-79081776	SK-N-SH_RA	brain:	n/a	n/a
2	EGR1	chr7:79081622-79081785	K562	blood:	n/a	n/a
3	REST	chr7:79081338-79081800	SK-N-SH	brain:	n/a	n/a
4	E2F6	chr7:79081447-79081976	H1-hESC	embryonic stem cell:	n/a	chr7:79081833-79081843
5	POLR2A	chr7:79081262-79081863	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:79081292-79082058	U87	brain:	n/a	n/a
7	POLR2A	chr7:79081448-79081759	A549	lung:	n/a	n/a
8	CEBPB	chr7:79081543-79081769	IMR90	lung:	n/a	n/a
9	CREB1	chr7:79081415-79081884	A549	lung:	n/a	n/a
10	SIN3AK20	chr7:79081259-79081757	PFSK-1	brain:	n/a	n/a
11	ATF3	chr7:79081448-79081794	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr7:79081492-79081952	ECC-1	luminal epithelium:	n/a	chr7:79081818-79081828
13	USF1	chr7:79081339-79082110	SK-N-SH	brain:	n/a	chr7:79081666-79081675 chr7:79081664-79081677 chr7:79081667-79081676 chr7:79081666-79081675
14	TBP	chr7:79081187-79082337	HepG2	liver:	n/a	n/a
15	JUND	chr7:79081498-79081839	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr7:79081127-79084617	HepG2	liver:	n/a	n/a
17	POLR2A	chr7:79081159-79082487	HepG2	liver:	n/a	n/a
18	FOS	chr7:79081503-79081846	HUVEC	blood vessel:	n/a	n/a
19	ETS1	chr7:79081401-79081868	A549	lung:	n/a	chr7:79081620-79081631 chr7:79081704-79081715
20	CTCF	chr7:79081640-79081790	HCPEpiC	choroid plexus:	n/a	n/a
21	SIN3AK20	chr7:79081390-79081773	HepG2	liver:	n/a	n/a
22	POLR2A	chr7:79081015-79084420	IMR90	lung:	n/a	n/a
23	MAX	chr7:79081395-79081951	ECC-1	luminal epithelium:	n/a	n/a
24	FOXA1	chr7:79081398-79081855	HepG2	liver:	n/a	n/a
25	CEBPB	chr7:79081011-79081880	HepG2	liver:	n/a	n/a
26	MYC	chr7:79081043-79082245	A549	lung:	n/a	n/a
27	HNF4A	chr7:79081305-79081835	HepG2	liver:	n/a	n/a
28	MAX	chr7:79081105-79082266	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr7:79081357-79081939	Gliobla	brain:	n/a	n/a
30	TAF1	chr7:79081193-79082353	PFSK-1	brain:	n/a	n/a
31	HDAC2	chr7:79081274-79081785	HepG2	liver:	n/a	n/a
32	CHD2	chr7:79081227-79082627	HepG2	liver:	n/a	chr7:79081620-79081630
33	JUND	chr7:79081577-79081737	H1-hESC	embryonic stem cell:	n/a	n/a
34	BHLHE40	chr7:79081520-79081884	A549	lung:	n/a	chr7:79081666-79081675 chr7:79081664-79081677 chr7:79081667-79081676 chr7:79081666-79081675
35	REST	chr7:79081404-79081854	SK-N-SH	brain:	n/a	n/a
36	MAX	chr7:79081325-79081870	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIN3AK20	chr7:79081253-79081816	PFSK-1	brain:	n/a	n/a
38	MAX	chr7:79081219-79082511	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr7:79081231-79081983	HUVEC	blood vessel:	n/a	n/a
40	MYC	chr7:79081497-79081794	HepG2	liver:	n/a	n/a
41	TAF1	chr7:79081370-79082117	SK-N-SH	brain:	n/a	n/a
42	MAZ	chr7:79081282-79083965	HepG2	liver:	n/a	chr7:79083803-79083813
43	POLR2A	chr7:79081404-79081829	ECC-1	luminal epithelium:	n/a	n/a
44	USF1	chr7:79081275-79082177	SK-N-SH_RA	brain:	n/a	chr7:79081666-79081675 chr7:79081664-79081677 chr7:79081667-79081676 chr7:79081666-79081675
45	POLR2A	chr7:79081442-79081768	ECC-1	luminal epithelium:	n/a	n/a
46	TCF7L2	chr7:79081174-79082961	PANC-1	pancreas:	n/a	n/a
47	TEAD4	chr7:79081054-79081819	HepG2	liver:	n/a	n/a
48	USF1	chr7:79081362-79082015	ECC-1	luminal epithelium:	n/a	chr7:79081666-79081675 chr7:79081664-79081677 chr7:79081667-79081676 chr7:79081666-79081675
49	FOXA1	chr7:79081219-79081781	HepG2	liver:	n/a	n/a
50	USF1	chr7:79081482-79081886	A549	lung:	n/a	chr7:79081666-79081675 chr7:79081664-79081677 chr7:79081667-79081676 chr7:79081666-79081675

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:79081666-79081716	GM12891	blood:	n/a
2	chr7:79081666-79081716	HCM	heart:	n/a
3	chr7:79081670-79081720	Hepatocyte	liver:	n/a
4	chr7:79081670-79081720	PFSK-1	brain:	n/a
5	chr7:79081670-79081720	ProgFib	skin:	n/a
6	chr7:79081670-79081720	U87	brain:	n/a
7	chr7:79081666-79081716	GM06990	blood:	n/a
8	chr7:79081670-79081720	BJ	skin:	n/a
9	chr7:79081670-79081720	SK-N-MC	brain:	n/a
10	chr7:79081670-79081720	HCPEpiC	choroid plexus:	n/a
11	chr7:79081666-79081716	HCPEpiC	choroid plexus:	n/a
12	chr7:79081666-79081716	HepG2	liver:	n/a
13	chr7:79081670-79081720	AG04450	lung:	fetal
14	chr7:79081670-79081720	HCF	heart:	n/a
15	chr7:79081666-79081716	Hepatocyte	liver:	n/a
16	chr7:79081670-79081720	GM12878	blood:	n/a
17	chr7:79081666-79081716	GM12878	blood:	n/a
18	chr7:79081670-79081720	HCM	heart:	n/a
19	chr7:79081666-79081716	Caco-2	colon:	n/a
20	chr7:79081670-79081720	Hela-S3	cervix:	n/a
21	chr7:79081670-79081720	SK-N-SH_RA	brain:	n/a
22	chr7:79081666-79081716	SK-N-MC	brain:	n/a
23	chr7:79081666-79081716	HRCEpiC	kidney:	n/a
24	chr7:79081670-79081720	HL-60	blood:	n/a
25	chr7:79081670-79081720	HRE	kidney:	n/a
26	chr7:79081666-79081716	NHBE	bronchial:	n/a
27	chr7:79081666-79081716	H1-hESC	embryonic stem cell:	embryo
28	chr7:79081670-79081720	NB4	blood:	n/a
29	chr7:79081666-79081716	MCF10A-Er-Src	breast:	n/a
30	chr7:79081666-79081716	Hela-S3	cervix:	n/a
31	chr7:79081666-79081716	GM12892	blood:	n/a
32	chr7:79081666-79081716	NB4	blood:	n/a
33	chr7:79081666-79081716	K562	blood:	n/a
34	chr7:79081670-79081720	HAEpiC	amniotic membrane:	n/a
35	chr7:79081670-79081720	GM19239	blood:	n/a
36	chr7:79081670-79081720	BE2_C	brain:	n/a
37	chr7:79081666-79081716	AoSMC	blood vessel:	n/a
38	chr7:79081666-79081716	AG04449	skin:	fetal
39	chr7:79081670-79081720	H1-hESC	embryonic stem cell:	embryo
40	chr7:79081670-79081720	HRCEpiC	kidney:	n/a
41	chr7:79081670-79081720	ovcar-3	ovarian:	n/a
42	chr7:79081666-79081716	HUVEC	blood vessel:	n/a
43	chr7:79081670-79081720	HEEpiC	esophagus:	n/a
44	chr7:79081670-79081720	PrEC	prostate:	n/a
45	chr7:79081670-79081720	HCT-116	colon:	n/a
46	chr7:79081670-79081720	CMK	blood:	n/a
47	chr7:79081670-79081720	AoSMC	blood vessel:	n/a
48	chr7:79081670-79081720	HIPEpiC	eye:	n/a
49	chr7:79081670-79081720	T-47D	breast:	n/a
50	chr7:79081666-79081716	HCF	heart:	n/a

Variant related genes	Relation type
MAGI2-AS3	TF binding region
MAGI2-AS3	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10273298	0.86[ASN][1000 genomes]
rs10953862	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10953863	0.86[ASN][1000 genomes]
rs12530628	0.82[ASN][1000 genomes]
rs2190168	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4730828	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4730829	0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4730831	0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4730836	0.84[ASN][1000 genomes]
rs4730870	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6466649	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6964700	0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs984708	0.83[JPT][hapmap]
rs991855	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv427792	chr7:79039802-79253373	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv970902	chr7:79046674-79175610	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79079800-79084600	Active TSS	NHLF	lung
2	chr7:79080200-79084000	Active TSS	Brain Anterior Caudate	brain
3	chr7:79080400-79084400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:79080400-79084600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:79080600-79084200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:79080600-79084400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:79080800-79082200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:79080800-79082400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:79080800-79083000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:79080800-79084000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:79080800-79084000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:79080800-79084400	Active TSS	Brain Hippocampus Middle	brain
13	chr7:79080800-79084400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr7:79080800-79084600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:79080800-79084600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:79080800-79084600	Active TSS	NHDF-Ad	bronchial
17	chr7:79081000-79081800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:79081000-79082000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr7:79081000-79082200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr7:79081000-79082400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:79081000-79082400	Active TSS	Stomach Smooth Muscle	stomach
22	chr7:79081000-79082400	Active TSS	HSMMtube	muscle
23	chr7:79081000-79082600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:79081000-79083800	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr7:79081000-79084000	Active TSS	Rectal Smooth Muscle	rectum
26	chr7:79081000-79084200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr7:79081000-79084200	Active TSS	Placenta Amnion	Placenta Amnion
28	chr7:79081000-79084200	Bivalent/Poised TSS	HepG2	liver
29	chr7:79081000-79084400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:79081000-79084400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:79081000-79084400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr7:79081000-79084400	Active TSS	Brain Substantia Nigra	brain
33	chr7:79081000-79084400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr7:79081000-79084400	Active TSS	Fetal Stomach	stomach
35	chr7:79081000-79084400	Active TSS	Left Ventricle	heart
36	chr7:79081000-79084400	Active TSS	Ovary	ovary
37	chr7:79081000-79084400	Active TSS	Right Ventricle	heart
38	chr7:79081000-79084600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr7:79081000-79084600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr7:79081000-79084600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr7:79081000-79084800	Active TSS	Aorta	Aorta
42	chr7:79081000-79084800	Active TSS	Right Atrium	heart
43	chr7:79081200-79081800	Active TSS	Primary hematopoietic stem cells	blood
44	chr7:79081200-79081800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
45	chr7:79081200-79081800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr7:79081200-79082000	Active TSS	HSMM	muscle
47	chr7:79081200-79082400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:79081200-79082400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:79081200-79082400	Active TSS	Osteobl	bone
50	chr7:79081200-79082800	Flanking Active TSS	Fetal Muscle Leg	muscle

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