Variant report

Variant	rs1269640
Chromosome Location	chr7:107886413-107886414
allele	A/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	EP300	chr7:107886125-107887566	A549	lung:	n/a	chr7:107887022-107887036 chr7:107886142-107886156 chr7:107886292-107886306
2	POLR2A	chr7:107886393-107886496	A549	lung:	n/a	n/a
3	TAF1	chr7:107886256-107886962	A549	lung:	n/a	n/a
4	SP1	chr7:107886403-107887302	HCT-116	colon:	n/a	n/a
5	USF1	chr7:107886337-107887250	A549	lung:	n/a	n/a
6	EP300	chr7:107886254-107887339	ECC-1	luminal epithelium:	n/a	chr7:107887022-107887036 chr7:107886292-107886306
7	TRIM28	chr7:107886335-107887484	K562	blood:	n/a	n/a
8	RCOR1	chr7:107886327-107887295	K562	blood:	n/a	n/a
9	MAX	chr7:107886168-107887682	A549	lung:	n/a	n/a
10	TCF12	chr7:107886357-107887257	ECC-1	luminal epithelium:	n/a	n/a
11	CEBPB	chr7:107886076-107887452	A549	lung:	n/a	chr7:107886144-107886157
12	POLR2A	chr7:107886230-107887143	U87	brain:	n/a	n/a
13	NR2F2	chr7:107886328-107887499	K562	blood:	n/a	chr7:107886916-107886931
14	ELF1	chr7:107886365-107887196	A549	lung:	n/a	n/a
15	EP300	chr7:107886302-107887395	A549	lung:	n/a	chr7:107887022-107887036
16	BACH1	chr7:107886143-107887454	K562	blood:	n/a	n/a
17	REST	chr7:107886330-107887287	A549	lung:	n/a	n/a
18	MAX	chr7:107886079-107887723	A549	lung:	n/a	n/a
19	BCL3	chr7:107886072-107887544	A549	lung:	n/a	n/a
20	MAX	chr7:107886354-107887445	A549	lung:	n/a	n/a
21	GTF2F1	chr7:107886396-107887158	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr7:107886366-107886506	A549	lung:	n/a	n/a
23	SMC3	chr7:107886356-107887253	Hela-S3	cervix:	n/a	n/a
24	TBL1XR1	chr7:107886103-107887278	K562	blood:	n/a	n/a
25	NR3C1	chr7:107886387-107887312	A549	lung:	n/a	chr7:107886887-107886896
26	TEAD4	chr7:107886215-107887535	K562	blood:	n/a	n/a
27	CEBPB	chr7:107886055-107887314	A549	lung:	n/a	chr7:107886144-107886157
28	POLR2A	chr7:107886248-107887341	HUVEC	blood vessel:	n/a	n/a
29	GATA3	chr7:107886070-107887432	A549	lung:	n/a	chr7:107886968-107886979 chr7:107886885-107886894
30	MAFK	chr7:107886310-107887722	K562	blood:	n/a	chr7:107886888-107886897 chr7:107886890-107886901
31	SP1	chr7:107886093-107887490	A549	lung:	n/a	n/a
32	FOSL2	chr7:107886039-107887485	A549	lung:	n/a	chr7:107886883-107886894 chr7:107886886-107886896 chr7:107886887-107886895 chr7:107886885-107886897 chr7:107887051-107887060 chr7:107886953-107886960 chr7:107886707-107886718 chr7:107886886-107886896
33	NFIC	chr7:107886399-107887254	ECC-1	luminal epithelium:	n/a	n/a
34	NR2F2	chr7:107886397-107887321	K562	blood:	n/a	chr7:107886916-107886931
35	CUX1	chr7:107886280-107887848	K562	blood:	n/a	n/a
36	BCL3	chr7:107886365-107887499	A549	lung:	n/a	n/a
37	CEBPB	chr7:107886026-107887279	IMR90	lung:	n/a	chr7:107886144-107886157
38	RAD21	chr7:107886349-107887292	A549	lung:	n/a	chr7:107886997-107887009
39	MAFK	chr7:107886251-107887175	IMR90	lung:	n/a	chr7:107886888-107886897 chr7:107886890-107886901
40	TCF12	chr7:107886354-107887337	ECC-1	luminal epithelium:	n/a	n/a
41	YY1	chr7:107886362-107887100	A549	lung:	n/a	n/a
42	EP300	chr7:107886362-107887347	K562	blood:	n/a	chr7:107887022-107887036
43	TCF12	chr7:107886101-107887525	A549	lung:	n/a	n/a
44	SIX5	chr7:107886048-107887777	A549	lung:	n/a	n/a
45	POLR2A	chr7:107886372-107886551	A549	lung:	n/a	n/a
46	POLR2A	chr7:107886357-107886803	A549	lung:	n/a	n/a
47	SMARCB1	chr7:107886286-107887312	K562	blood:	n/a	chr7:107886886-107886895
48	TEAD4	chr7:107886314-107887186	K562	blood:	n/a	n/a
49	EP300	chr7:107886405-107887184	ECC-1	luminal epithelium:	n/a	chr7:107887022-107887036
50	SP1	chr7:107886239-107887353	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:107885403..107887866-chr7:108208741..108211380,3	K562	blood:
2	chr7:107885138..107886888-chr7:108093240..108094894,2	K562	blood:
3	chr7:107844217..107846862-chr7:107884511..107886903,2	K562	blood:
4	chr7:107880432..107884512-chr7:107884667..107887859,3	MCF-7	breast:
5	chr7:107885764..107888071-chr7:107990459..107993788,3	MCF-7	breast:
6	chr7:107883815..107886718-chr7:108095136..108097625,2	MCF-7	breast:
7	chr7:107885444..107889446-chr7:107936320..107941216,4	MCF-7	breast:

Variant related genes	Relation type
NRCAM	TF binding region
ENSG00000177683	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1155	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs1269621	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1269622	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1269623	0.89[EUR][1000 genomes]
rs1269625	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1269628	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1269629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1269634	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269639	0.92[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269641	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269642	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1269643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269645	0.96[CEU][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1269649	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1269650	0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs1269651	0.85[AMR][1000 genomes]
rs1269652	0.81[EUR][1000 genomes]
rs1269653	0.81[EUR][1000 genomes]
rs1269655	0.84[AMR][1000 genomes]
rs1269656	0.83[AMR][1000 genomes]
rs1269659	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs2284284	0.81[JPT][hapmap]
rs36065373	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs370133	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs3819747	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs405945	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs422011	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6970096	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs926146	0.92[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:107880600-107887000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:107880800-107886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:107881200-107886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:107883600-107886800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:107884800-107890600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:107885600-107887000	Enhancers	HSMM	muscle
8	chr7:107885600-107888400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:107885600-107889400	Enhancers	Osteobl	bone
10	chr7:107885800-107887600	Flanking Active TSS	A549	lung
11	chr7:107885800-107887600	Enhancers	NHLF	lung
12	chr7:107885800-107888400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:107886000-107887600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:107886000-107891200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr7:107886200-107886600	Flanking Active TSS	NH-A	brain
16	chr7:107886200-107886800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:107886200-107886800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:107886200-107886800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:107886200-107886800	Flanking Active TSS	NHDF-Ad	bronchial
20	chr7:107886200-107887400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:107886200-107887400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr7:107886200-107887600	Enhancers	Hela-S3	cervix
23	chr7:107886200-107887800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:107886200-107889400	Enhancers	HMEC	breast
25	chr7:107886200-107889600	Enhancers	HUVEC	blood vessel
26	chr7:107886400-107886600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:107886400-107886600	Enhancers	Spleen	Spleen
28	chr7:107886400-107886800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:107886400-107886800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr7:107886400-107886800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:107886400-107886800	Flanking Active TSS	HSMMtube	muscle
32	chr7:107886400-107886800	Transcr. at gene 5' and 3'	K562	blood
33	chr7:107886400-107887000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr7:107886400-107887000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:107886400-107887000	Enhancers	Adipose Nuclei	Adipose
36	chr7:107886400-107887200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr7:107886400-107887200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr7:107886400-107887200	Enhancers	Fetal Kidney	kidney
39	chr7:107886400-107887200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr7:107886400-107887400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:107886400-107887400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr7:107886400-107887400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr7:107886400-107887400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:107886400-107887400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:107886400-107887400	Enhancers	Fetal Intestine Small	intestine
46	chr7:107886400-107887400	Enhancers	Pancreas	Pancrea
47	chr7:107886400-107887600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:107886400-107887600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:107886400-107887600	Enhancers	Brain Anterior Caudate	brain
50	chr7:107886400-107887600	Enhancers	HepG2	liver

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