Variant report

Variant	rs7577879
Chromosome Location	chr2:39740804-39740805
allele	G/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	POU2F2	chr2:39740672-39741157	GM12891	blood:	n/a	n/a
2	EP300	chr2:39740664-39741138	SK-N-SH_RA	brain:	n/a	chr2:39741029-39741036
3	ARID3A	chr2:39740784-39741147	HepG2	liver:	n/a	n/a
4	RAD21	chr2:39740689-39741228	MCF-7	breast:	n/a	chr2:39740968-39740987
5	NFIC	chr2:39740674-39741198	HepG2	liver:	n/a	n/a
6	TEAD4	chr2:39740631-39741269	HepG2	liver:	n/a	n/a
7	CTCF	chr2:39740746-39741179	HepG2	liver:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
8	JUND	chr2:39740804-39741188	HepG2	liver:	n/a	n/a
9	RAD21	chr2:39740603-39741397	A549	lung:	n/a	chr2:39740968-39740987
10	ATF2	chr2:39740583-39741083	GM12878	blood:	n/a	n/a
11	BCL3	chr2:39740747-39741043	GM12878	blood:	n/a	chr2:39740846-39740855 chr2:39740845-39740854
12	CTCF	chr2:39740757-39741153	A549	lung:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
13	POLR2A	chr2:39740617-39741127	SK-N-SH	brain:	n/a	n/a
14	TAF1	chr2:39740740-39741106	PFSK-1	brain:	n/a	n/a
15	BCL11A	chr2:39740726-39741017	GM12878	blood:	n/a	chr2:39740846-39740855 chr2:39740845-39740854
16	EGR1	chr2:39740681-39741133	K562	blood:	n/a	n/a
17	STAT3	chr2:39740752-39741125	MCF10A-Er-Src	breast:	n/a	chr2:39740845-39740854 chr2:39740846-39740855 chr2:39740852-39740863
18	CTCF	chr2:39740744-39741154	K562	blood:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
19	CTCF	chr2:39740055-39741404	A549	lung:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
20	CTCF	chr2:39740698-39741270	MCF-7	breast:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
21	SIN3A	chr2:39740803-39741077	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr2:39740627-39741178	SK-N-SH_RA	brain:	n/a	chr2:39740968-39740987
23	RAD21	chr2:39740782-39741071	GM12878	blood:	n/a	chr2:39740968-39740987
24	RELA	chr2:39740692-39741295	GM12891	blood:	n/a	n/a
25	JUN	chr2:39740529-39741144	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr2:39740680-39741127	IMR90	lung:	n/a	n/a
27	RAD21	chr2:39740704-39741207	A549	lung:	n/a	chr2:39740968-39740987
28	BCLAF1	chr2:39740706-39741111	GM12878	blood:	n/a	chr2:39740846-39740855 chr2:39740845-39740854
29	IKZF1	chr2:39740670-39741130	GM12878	blood:	n/a	n/a
30	MYC	chr2:39740803-39741128	MCF10A-Er-Src	breast:	n/a	n/a
31	RAD21	chr2:39740762-39741092	H1-hESC	embryonic stem cell:	n/a	chr2:39740968-39740987
32	GATA2	chr2:39740528-39741408	HUVEC	blood vessel:	n/a	chr2:39741274-39741281
33	SMC3	chr2:39740767-39741198	Hela-S3	cervix:	n/a	chr2:39740969-39740983
34	PBX3	chr2:39740572-39741249	SK-N-SH	brain:	n/a	n/a
35	FOS	chr2:39740679-39741207	MCF10A-Er-Src	breast:	n/a	chr2:39740844-39740855
36	RAD21	chr2:39740795-39741216	A549	lung:	n/a	chr2:39740968-39740987
37	BCL11A	chr2:39740642-39741071	GM12878	blood:	n/a	chr2:39740846-39740855 chr2:39740845-39740854
38	RAD21	chr2:39740674-39741265	HCT-116	colon:	n/a	chr2:39740968-39740987
39	MAFK	chr2:39740733-39741205	K562	blood:	n/a	n/a
40	ATF2	chr2:39740531-39741202	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:39740588-39741261	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr2:39740528-39742023	SK-N-SH	brain:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
43	SP1	chr2:39740708-39741100	GM12878	blood:	n/a	n/a
44	MTA3	chr2:39740558-39741170	GM12878	blood:	n/a	n/a
45	CTCF	chr2:39740801-39741127	SK-N-SH_RA	brain:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
46	IRF4	chr2:39740632-39741076	GM12878	blood:	n/a	n/a
47	PAX5	chr2:39740718-39741144	GM12878	blood:	n/a	n/a
48	RAD21	chr2:39740788-39741255	HepG2	liver:	n/a	chr2:39740968-39740987
49	IRF4	chr2:39740681-39741115	GM12878	blood:	n/a	n/a
50	RAD21	chr2:39740797-39741046	K562	blood:	n/a	chr2:39740968-39740987

No.	Distal block	Cell Line	Cell type
1	chr2:39738702..39740814-chr2:39742603..39745081,2	MCF-7	breast:
2	chr2:39662573..39664202-chr2:39738821..39741104,2	K562	blood:
3	chr2:39740456..39741440-chr2:39923994..39925288,5	MCF-7	breast:
4	chr2:39739040..39741917-chr2:40004865..40006467,2	K562	blood:
5	chr2:39661305..39663930-chr2:39740460..39742003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000138050	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000152154	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11124685	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs7591326	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
2	chr2:39724800-39750600	Weak transcription	Gastric	stomach
3	chr2:39731000-39741400	Enhancers	Fetal Stomach	stomach
4	chr2:39731200-39741400	Enhancers	Fetal Lung	lung
5	chr2:39732800-39741400	Enhancers	NHLF	lung
6	chr2:39733000-39743600	Weak transcription	Hela-S3	cervix
7	chr2:39733600-39741400	Enhancers	Colon Smooth Muscle	Colon
8	chr2:39733800-39741600	Enhancers	Fetal Kidney	kidney
9	chr2:39734200-39741400	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:39734600-39745000	Enhancers	Adipose Nuclei	Adipose
11	chr2:39734600-39746000	Enhancers	Fetal Heart	heart
12	chr2:39735000-39744800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:39736400-39741200	Enhancers	Fetal Intestine Small	intestine
14	chr2:39736400-39741600	Enhancers	Ovary	ovary
15	chr2:39736400-39741800	Enhancers	HepG2	liver
16	chr2:39736400-39742000	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:39736400-39745000	Enhancers	Right Atrium	heart
18	chr2:39736400-39745000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:39736600-39741800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:39736800-39741600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:39737000-39744800	Enhancers	Fetal Muscle Leg	muscle
22	chr2:39737000-39745000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39737200-39741600	Enhancers	Placenta	Placenta
24	chr2:39737400-39743000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:39738000-39745000	Enhancers	Duodenum Mucosa	Duodenum
26	chr2:39738200-39741400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:39738200-39741400	Enhancers	Stomach Smooth Muscle	stomach
28	chr2:39738200-39741600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:39738200-39741600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:39738200-39741600	Enhancers	NHDF-Ad	bronchial
31	chr2:39738400-39741400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:39738400-39741400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:39738400-39741400	Enhancers	Psoas Muscle	Psoas
34	chr2:39738400-39741600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:39738400-39741600	Enhancers	Stomach Mucosa	stomach
36	chr2:39738400-39741800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:39738400-39741800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:39738400-39742000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:39738800-39741400	Weak transcription	Spleen	Spleen
40	chr2:39738800-39741600	Enhancers	Osteobl	bone
41	chr2:39738800-39741800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:39738800-39743000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:39738800-39743000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:39739000-39741600	Enhancers	HSMMtube	muscle
45	chr2:39739200-39741200	Enhancers	Small Intestine	intestine
46	chr2:39739400-39741400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr2:39739400-39743600	Enhancers	HUVEC	blood vessel
48	chr2:39739600-39741400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:39739600-39741400	Enhancers	HSMM	muscle
50	chr2:39739600-39742600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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