Variant report

Variant	rs16861180
Chromosome Location	chr2:173886635-173886636
allele	C/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	CTCF	chr2:173886486-173887145	HCT-116	colon:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
2	CEBPB	chr2:173886519-173886957	MCF-7	breast:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
3	CTCF	chr2:173886617-173886995	K562	blood:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
4	RAD21	chr2:173886518-173887090	A549	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
5	JUND	chr2:173886584-173886812	K562	blood:	n/a	n/a
6	RAD21	chr2:173886613-173886998	A549	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
7	FOS	chr2:173886587-173886878	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:173886625-173886933	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr2:173886600-173886750	WI-38	lung:	n/a	n/a
10	CTCF	chr2:173886166-173887245	A549	lung:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
11	CEBPB	chr2:173886495-173887035	MCF-7	breast:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
12	FOS	chr2:173886589-173886883	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr2:173886540-173886690	SK-N-SH_RA	brain:	n/a	n/a
14	CEBPB	chr2:173886555-173886907	A549	lung:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
15	CEBPB	chr2:173886588-173886984	Hela-S3	cervix:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
16	RAD21	chr2:173886453-173887020	HepG2	liver:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
17	CTCF	chr2:173886628-173886943	HepG2	liver:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
18	CTCF	chr2:173886518-173887144	MCF-7	breast:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
19	SMC3	chr2:173886497-173887029	Hela-S3	cervix:	n/a	chr2:173886800-173886814
20	RAD21	chr2:173886560-173887061	H1-hESC	embryonic stem cell:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
21	RAD21	chr2:173886615-173886984	SK-N-SH_RA	brain:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
22	CEBPB	chr2:173886542-173886961	A549	lung:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
23	CTCF	chr2:173886599-173886925	Medullo	brain:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
24	STAT3	chr2:173886486-173886897	MCF10A-Er-Src	breast:	n/a	chr2:173886812-173886823
25	CEBPB	chr2:173886588-173886895	K562	blood:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
26	ARID3A	chr2:173886550-173886955	HepG2	liver:	n/a	n/a
27	CEBPB	chr2:173886585-173886914	K562	blood:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
28	CEBPB	chr2:173886589-173886962	HepG2	liver:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
29	CEBPB	chr2:173886579-173886954	IMR90	lung:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
30	SP1	chr2:173886531-173887078	A549	lung:	n/a	n/a
31	TCF12	chr2:173886477-173887117	A549	lung:	n/a	n/a
32	E2F4	chr2:173886406-173886929	MCF10A-Er-Src	breast:	n/a	chr2:173886606-173886620
33	RAD21	chr2:173886484-173887043	MCF-7	breast:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
34	RAD21	chr2:173886605-173886971	HepG2	liver:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
35	RAD21	chr2:173886428-173887096	A549	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
36	SMC3	chr2:173886568-173887021	HepG2	liver:	n/a	chr2:173886800-173886814
37	RAD21	chr2:173886402-173887052	MCF-7	breast:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
38	CTCF	chr2:173886558-173887004	HepG2	liver:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
39	CTCF	chr2:173886519-173887025	A549	lung:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
40	CEBPB	chr2:173886495-173887064	A549	lung:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
41	CTCF	chr2:173886602-173887026	IMR90	lung:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
42	CTCF	chr2:173886595-173886996	A549	lung:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
43	RAD21	chr2:173886462-173887062	HCT-116	colon:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
44	STAT3	chr2:173886597-173886896	MCF10A-Er-Src	breast:	n/a	chr2:173886812-173886823
45	CTCF	chr2:173886453-173887171	SK-N-SH	brain:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
46	CTCF	chr2:173886497-173887075	MCF-7	breast:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
47	RAD21	chr2:173886602-173886990	Hela-S3	cervix:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
48	RAD21	chr2:173886467-173887267	SK-N-SH	brain:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
49	RAD21	chr2:173886578-173887021	IMR90	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
50	RAD21	chr2:173886618-173886994	HepG2	liver:	n/a	chr2:173886796-173886815 chr2:173886799-173886812

No.	Distal block	Cell Line	Cell type
1	chr2:173841835..173842797-chr2:173886338..173887289,8	MCF-7	breast:
2	chr2:173840817..173843158-chr2:173885041..173887379,4	MCF-7	breast:
3	chr2:173729672..173730467-chr2:173886391..173887246,2	MCF-7	breast:
4	chr2:173885808..173888407-chr2:173907815..173910951,3	MCF-7	breast:
5	chr2:173841773..173843105-chr2:173886256..173887211,13	MCF-7	breast:
6	chr2:173867155..173868911-chr2:173885451..173888088,2	MCF-7	breast:
7	chr2:173836656..173837372-chr2:173886327..173887177,4	MCF-7	breast:
8	chr2:173670836..173671405-chr2:173886290..173887243,2	MCF-7	breast:
9	chr2:173796378..173796920-chr2:173886314..173886946,2	MCF-7	breast:
10	chr2:173885113..173887445-chr2:173889594..173892152,2	K562	blood:
11	chr2:173847799..173849946-chr2:173883795..173886644,2	MCF-7	breast:
12	chr2:173836694..173837365-chr2:173886317..173887226,2	K562	blood:

Variant related genes	Relation type
RAPGEF4	TF binding region
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12612593	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12614386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615974	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12618296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034647	1.00[AFR][1000 genomes]
rs16861185	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861206	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34252442	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35730673	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3769218	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769219	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs3769221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3769223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268707	1.00[AFR][1000 genomes]
rs4296399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7585995	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173835800-173886800	Weak transcription	Lung	lung
2	chr2:173856200-173892600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:173861000-173888000	Weak transcription	Fetal Stomach	stomach
4	chr2:173868000-173902000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:173868600-173892200	Weak transcription	Fetal Intestine Large	intestine
6	chr2:173877200-173901600	Weak transcription	Gastric	stomach
7	chr2:173877800-173887800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:173879400-173888600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:173880800-173891600	Strong transcription	Liver	Liver
10	chr2:173881200-173892400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:173881400-173887200	Weak transcription	Esophagus	oesophagus
13	chr2:173881400-173897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:173883000-173887000	Weak transcription	Left Ventricle	heart
15	chr2:173883000-173892200	Weak transcription	Right Atrium	heart
16	chr2:173883200-173886800	Weak transcription	Adipose Nuclei	Adipose
17	chr2:173884400-173886800	Weak transcription	Ovary	ovary
18	chr2:173884600-173887000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:173884800-173893000	Weak transcription	Right Ventricle	heart
20	chr2:173885400-173890800	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:173885400-173892000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:173885400-173892600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:173885800-173887000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:173886000-173888000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:173886200-173887800	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:173886200-173890000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:173886400-173887000	Flanking Active TSS	A549	lung
28	chr2:173886400-173887200	Enhancers	Hela-S3	cervix
29	chr2:173886400-173887400	Enhancers	Fetal Heart	heart
30	chr2:173886600-173886800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:173886600-173887000	Enhancers	Fetal Lung	lung
32	chr2:173886600-173887200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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