Variant report

Variant	rs28902199
Chromosome Location	chr2:234886080-234886081
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	chr2:234886030-234886433	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr2:234885995-234886496	SK-N-SH	brain:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
3	REST	chr2:234886056-234886496	HCT-116	colon:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
4	SMC3	chr2:234885334-234886250	HepG2	liver:	n/a	n/a
5	REST	chr2:234885882-234886539	ECC-1	luminal epithelium:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
6	SP1	chr2:234885262-234886414	A549	lung:	n/a	n/a
7	CEBPB	chr2:234885250-234886267	A549	lung:	n/a	chr2:234885941-234885954
8	REST	chr2:234886033-234886479	PANC-1	pancreas:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
9	RAD21	chr2:234885112-234886347	A549	lung:	n/a	chr2:234885393-234885405
10	RAD21	chr2:234885279-234886378	A549	lung:	n/a	chr2:234885393-234885405
11	REST	chr2:234885275-234886644	A549	lung:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297 chr2:234885595-234885605
12	REST	chr2:234886018-234886431	PFSK-1	brain:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
13	REST	chr2:234886062-234886411	HL-60	blood:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
14	REST	chr2:234886068-234886375	PANC-1	pancreas:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
15	EP300	chr2:234885269-234886532	A549	lung:	n/a	chr2:234885274-234885288 chr2:234885639-234885653 chr2:234885939-234885953 chr2:234886150-234886166 chr2:234885519-234885533
16	REST	chr2:234886048-234886498	HepG2	liver:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
17	SMC3	chr2:234884896-234886581	SK-N-SH	brain:	n/a	n/a
18	CEBPB	chr2:234885518-234886123	HepG2	liver:	n/a	chr2:234885941-234885954
19	REST	chr2:234885883-234886560	PANC-1	pancreas:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
20	EP300	chr2:234885208-234886154	A549	lung:	n/a	chr2:234885274-234885288 chr2:234885639-234885653 chr2:234885939-234885953 chr2:234885519-234885533
21	REST	chr2:234885980-234886513	HCT-116	colon:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
22	REST	chr2:234886050-234886482	H1-hESC	embryonic stem cell:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
23	REST	chr2:234885996-234886468	U87	brain:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
24	RAD21	chr2:234884920-234886315	SK-N-SH	brain:	n/a	chr2:234885393-234885405
25	SP1	chr2:234885278-234886108	A549	lung:	n/a	n/a
26	REST	chr2:234885927-234886641	ECC-1	luminal epithelium:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
27	TCF12	chr2:234885069-234886157	A549	lung:	n/a	n/a
28	GATA3	chr2:234885131-234886147	A549	lung:	n/a	chr2:234885482-234885491 chr2:234885475-234885496 chr2:234886012-234886022
29	REST	chr2:234885981-234886531	PANC-1	pancreas:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
30	REST	chr2:234886080-234886452	MCF-7	breast:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
31	CEBPB	chr2:234885519-234886132	A549	lung:	n/a	chr2:234885941-234885954
32	REST	chr2:234886011-234886449	PFSK-1	brain:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
33	REST	chr2:234886006-234886500	A549	lung:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
34	REST	chr2:234886029-234886513	HL-60	blood:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297
35	CTCF	chr2:234885083-234886089	A549	lung:	n/a	chr2:234885502-234885523
36	CEBPB	chr2:234885543-234886130	IMR90	lung:	n/a	chr2:234885941-234885954
37	REST	chr2:234885998-234886468	U87	brain:	n/a	chr2:234886186-234886199 chr2:234886288-234886297 chr2:234886278-234886296 chr2:234886277-234886297

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

Variant related genes	Relation type
TRPM8	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs28901630	1.00[EUR][1000 genomes]
rs28902207	0.83[YRI][hapmap]
rs28902221	0.83[YRI][hapmap]
rs6756537	0.83[YRI][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	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234881600-234886400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:234881800-234886400	Enhancers	HMEC	breast
3	chr2:234881800-234886400	Enhancers	NHEK	skin
4	chr2:234881800-234886600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:234881800-234890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:234882200-234886200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr2:234882200-234886600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:234882400-234892200	Enhancers	NHLF	lung
9	chr2:234883600-234886400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:234883800-234886800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:234884200-234887600	Weak transcription	HSMM	muscle
12	chr2:234884200-234888000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:234884200-234888000	Weak transcription	Osteobl	bone
14	chr2:234884200-234888400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:234884200-234888400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:234884200-234889400	Weak transcription	HSMMtube	muscle
17	chr2:234885000-234886200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:234885000-234886400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:234885200-234886200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr2:234885200-234886200	Enhancers	Fetal Brain Male	brain
21	chr2:234885200-234886400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:234885200-234886400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:234885200-234887600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:234885200-234888000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:234885400-234886200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:234885400-234886400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:234885400-234887600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:234885400-234887600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:234885400-234887800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:234885600-234886200	Flanking Active TSS	HepG2	liver
31	chr2:234885600-234886400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:234885600-234886400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:234885600-234886400	Flanking Active TSS	A549	lung
34	chr2:234885600-234886600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:234885600-234886600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:234885600-234886600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:234885800-234886400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:234885800-234886400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:234885800-234886400	Enhancers	Pancreas	Pancrea
40	chr2:234885800-234887000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:234885800-234890000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:234886000-234886400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr2:234886000-234886600	Flanking Active TSS	Liver	Liver
44	chr2:234886000-234887600	Weak transcription	NHDF-Ad	bronchial
45	chr2:234886000-234888200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:234886000-234888200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:234886000-234889800	Weak transcription	NH-A	brain

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