Variant report

Variant	rs55888324
Chromosome Location	chr2:234472346-234472347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234472035..234473937-chr2:234616865..234619680,2	MCF-7	breast:
2	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:
3	chr2:234470715..234472722-chr2:234612737..234614853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224814	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs28968505	0.88[AFR][1000 genomes]
rs4047262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4281901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4392254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4588184	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56274731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56306918	1.00[AMR][1000 genomes]
rs56317380	1.00[AMR][1000 genomes]
rs57285092	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57768657	0.88[AFR][1000 genomes]
rs58330864	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58489211	1.00[AMR][1000 genomes]
rs58583213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58864422	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59543173	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59954119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61376069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726032	1.00[AMR][1000 genomes]
rs6734355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995922	1.00[AMR][1000 genomes]
rs73995923	1.00[AMR][1000 genomes]
rs73995944	1.00[AMR][1000 genomes]
rs73995946	1.00[AMR][1000 genomes]
rs73995947	1.00[AMR][1000 genomes]
rs73995948	1.00[AMR][1000 genomes]
rs73995949	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995950	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995970	1.00[AMR][1000 genomes]
rs73995972	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995973	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995974	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996105	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997606	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997607	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997608	1.00[AMR][1000 genomes]
rs73997611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997612	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997631	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997633	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997638	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs745154	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580191	1.00[AMR][1000 genomes]
rs7584192	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7593807	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv519876	chr2:234466843-234493048	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
2	chr2:234413000-234474200	Weak transcription	Fetal Heart	heart
3	chr2:234423200-234473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:234426200-234474000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:234428800-234474400	Weak transcription	Brain Germinal Matrix	brain
6	chr2:234430200-234473800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:234430800-234472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:234432200-234474800	Weak transcription	Spleen	Spleen
9	chr2:234432600-234474400	Weak transcription	Colonic Mucosa	Colon
10	chr2:234437200-234474400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:234441600-234474800	Weak transcription	Gastric	stomach
12	chr2:234442400-234474400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:234447800-234474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:234451200-234474200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:234453200-234474400	Weak transcription	Small Intestine	intestine
16	chr2:234453600-234474000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:234455400-234474400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:234456600-234474000	Weak transcription	Fetal Brain Male	brain
19	chr2:234457400-234474000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:234460600-234474000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:234461800-234474000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:234463000-234474200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:234463200-234473400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:234465800-234472400	Weak transcription	K562	blood
25	chr2:234466000-234474000	Weak transcription	Brain Substantia Nigra	brain
26	chr2:234466000-234474600	Weak transcription	Pancreas	Pancrea
27	chr2:234466200-234474200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:234466400-234472400	Weak transcription	Lung	lung
29	chr2:234466400-234474000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:234466400-234474200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:234466400-234474400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:234466400-234474400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:234466400-234474800	Weak transcription	Esophagus	oesophagus
34	chr2:234466600-234473400	Weak transcription	NHLF	lung
35	chr2:234466600-234474000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:234466600-234474000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:234466600-234474000	Weak transcription	NH-A	brain
38	chr2:234466600-234474200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:234466600-234474200	Weak transcription	Thymus	Thymus
40	chr2:234466600-234474400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:234466600-234474400	Weak transcription	Aorta	Aorta
42	chr2:234466600-234474400	Weak transcription	Brain Angular Gyrus	brain
43	chr2:234466600-234474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:234466800-234472400	Weak transcription	HSMMtube	muscle
45	chr2:234466800-234472800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:234466800-234472800	Weak transcription	HMEC	breast
47	chr2:234466800-234474400	Weak transcription	Ovary	ovary
48	chr2:234467400-234472400	Weak transcription	Left Ventricle	heart
49	chr2:234467400-234472800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:234467600-234472400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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