Variant report

Variant	rs28902198
Chromosome Location	chr2:234885511-234885512
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	chr2:234885400-234885550	BE2_C	brain:	n/a	chr2:234885502-234885523
2	CTCF	chr2:234885400-234885622	LNCaP	prostate:	n/a	chr2:234885502-234885523
3	RAD21	chr2:234885332-234885803	MCF-7	breast:	n/a	chr2:234885393-234885405
4	FOXA1	chr2:234885464-234885905	HepG2	liver:	n/a	chr2:234885850-234885862
5	CTCF	chr2:234885460-234885610	Caco-2	colon:	n/a	chr2:234885502-234885523
6	GATA2	chr2:234885300-234885655	HUVEC	blood vessel:	n/a	chr2:234885482-234885491 chr2:234885475-234885496
7	CTCF	chr2:234885430-234885590	K562	blood:	n/a	chr2:234885502-234885523
8	CTCF	chr2:234885465-234885551	Fibrobl	skin:	n/a	chr2:234885502-234885523
9	CTCF	chr2:234885480-234885630	GM06990	blood:	n/a	chr2:234885502-234885523
10	CTCF	chr2:234885380-234885530	BE2_C	brain:	n/a	chr2:234885502-234885523
11	CTCF	chr2:234885420-234885570	GM12801	blood:	n/a	chr2:234885502-234885523
12	ZNF143	chr2:234885354-234885669	GM12878	blood:	n/a	n/a
13	CTCF	chr2:234885440-234885590	AoAF	blood vessel:	n/a	chr2:234885502-234885523
14	CTCF	chr2:234885350-234885676	K562	blood:	n/a	chr2:234885502-234885523
15	CTCF	chr2:234885400-234885550	RPTEC	kidney:	n/a	chr2:234885502-234885523
16	MXI1	chr2:234885437-234885539	GM12878	blood:	n/a	n/a
17	SMC3	chr2:234885334-234886250	HepG2	liver:	n/a	n/a
18	RAD21	chr2:234885305-234885776	IMR90	lung:	n/a	chr2:234885393-234885405
19	CTCF	chr2:234885401-234885623	Gliobla	brain:	n/a	chr2:234885502-234885523
20	CTCF	chr2:234885420-234885570	HCPEpiC	choroid plexus:	n/a	chr2:234885502-234885523
21	CTCF	chr2:234885273-234885797	MCF-7	breast:	n/a	chr2:234885502-234885523
22	ELF1	chr2:234885460-234885891	HepG2	liver:	n/a	n/a
23	REST	chr2:234885345-234885728	A549	lung:	n/a	chr2:234885595-234885605
24	GATA3	chr2:234885215-234885699	SH-SY5Y	brain:	n/a	chr2:234885482-234885491 chr2:234885475-234885496
25	CTCF	chr2:234885420-234885570	AG09309	skin:	n/a	chr2:234885502-234885523
26	CTCF	chr2:234885406-234885623	T-47D	breast:	n/a	chr2:234885502-234885523
27	MYBL2	chr2:234885265-234886059	HepG2	liver:	n/a	n/a
28	RAD21	chr2:234885303-234885789	H1-hESC	embryonic stem cell:	n/a	chr2:234885393-234885405
29	CTCF	chr2:234885420-234885570	HRE	kidney:	n/a	chr2:234885502-234885523
30	CTCF	chr2:234885460-234885610	GM12865	blood:	n/a	chr2:234885502-234885523
31	CTCF	chr2:234885211-234885975	HCT-116	colon:	n/a	chr2:234885502-234885523
32	MAFF	chr2:234885433-234885930	HepG2	liver:	n/a	chr2:234885757-234885775
33	CTCF	chr2:234885374-234885640	MCF-7	breast:	n/a	chr2:234885502-234885523
34	CTCF	chr2:234885457-234885569	GM19239	blood:	n/a	chr2:234885502-234885523
35	RAD21	chr2:234885190-234885837	HCT-116	colon:	n/a	chr2:234885393-234885405
36	CTCF	chr2:234885295-234885622	H1-hESC	embryonic stem cell:	n/a	chr2:234885502-234885523
37	SP1	chr2:234885262-234886414	A549	lung:	n/a	n/a
38	CEBPB	chr2:234885250-234886267	A549	lung:	n/a	chr2:234885941-234885954
39	CTCF	chr2:234885420-234885570	HFF-Myc	foreskin:	n/a	chr2:234885502-234885523
40	CTCF	chr2:234885460-234885610	HRPEpiC	eye:	n/a	chr2:234885502-234885523
41	CTCF	chr2:234885460-234885610	HA-sp	spinal cord:	n/a	chr2:234885502-234885523
42	CTCF	chr2:234885460-234885610	GM12866	blood:	n/a	chr2:234885502-234885523
43	ZNF143	chr2:234885364-234885636	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr2:234885442-234885597	LNCaP	prostate:	n/a	chr2:234885502-234885523
45	CTCF	chr2:234885420-234885570	GM12874	blood:	n/a	chr2:234885502-234885523
46	RAD21	chr2:234885112-234886347	A549	lung:	n/a	chr2:234885393-234885405
47	RAD21	chr2:234885252-234885810	SK-N-SH_RA	brain:	n/a	chr2:234885393-234885405
48	SMC3	chr2:234885310-234885741	Hela-S3	cervix:	n/a	n/a
49	RAD21	chr2:234885279-234886378	A549	lung:	n/a	chr2:234885393-234885405
50	CTCF	chr2:234885425-234885701	A549	lung:	n/a	chr2:234885502-234885523

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234885292..234886125-chr2:235166874..235167410,2	MCF-7	breast:
2	chr2:234885184..234885936-chr2:235044485..235045118,2	MCF-7	breast:

Variant related genes	Relation type
TRPM8	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs28902219	0.85[YRI][hapmap]
rs28902228	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28903674	1.00[AMR][1000 genomes]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234880200-234885800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234881600-234886400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:234881800-234886000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:234881800-234886400	Enhancers	HMEC	breast
5	chr2:234881800-234886400	Enhancers	NHEK	skin
6	chr2:234881800-234886600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:234881800-234890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:234882200-234886200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:234882200-234886600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:234882400-234886000	Enhancers	NH-A	brain
11	chr2:234882400-234886000	Enhancers	NHDF-Ad	bronchial
12	chr2:234882400-234892200	Enhancers	NHLF	lung
13	chr2:234883600-234885600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:234883600-234886000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:234883600-234886400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:234883800-234885600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:234883800-234886800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:234884000-234885600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:234884200-234885600	Enhancers	A549	lung
20	chr2:234884200-234887600	Weak transcription	HSMM	muscle
21	chr2:234884200-234888000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:234884200-234888000	Weak transcription	Osteobl	bone
23	chr2:234884200-234888400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:234884200-234888400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:234884200-234889400	Weak transcription	HSMMtube	muscle
26	chr2:234884400-234885600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:234884600-234885600	Flanking Active TSS	Liver	Liver
28	chr2:234885000-234885600	Enhancers	HepG2	liver
29	chr2:234885000-234886200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:234885000-234886400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:234885200-234885600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:234885200-234886200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:234885200-234886200	Enhancers	Fetal Brain Male	brain
34	chr2:234885200-234886400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:234885200-234886400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:234885200-234887600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:234885200-234888000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:234885400-234885800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:234885400-234885800	Weak transcription	Pancreas	Pancrea
40	chr2:234885400-234886200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:234885400-234886400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr2:234885400-234887600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:234885400-234887600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:234885400-234887800	Enhancers	Primary T helper cells fromperipheralblood	blood

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