Variant report

Variant	rs6705519
Chromosome Location	chr2:55204165-55204166
allele	C/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	POLR2A	chr2:55203177-55204219	U87	brain:	n/a	n/a
2	NFIC	chr2:55204165-55204735	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:55203339-55204229	A549	lung:	n/a	n/a
4	ATF2	chr2:55204104-55204774	GM12878	blood:	n/a	n/a
5	SPI1	chr2:55204131-55204780	GM12878	blood:	n/a	chr2:55204556-55204563
6	POLR2A	chr2:55203189-55204245	U87	brain:	n/a	n/a
7	MEF2A	chr2:55204160-55204794	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:55201696-55205299	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55180338..55182211-chr2:55203492..55207061,3	MCF-7	breast:
2	chr2:55199321..55201590-chr2:55202195..55204669,2	MCF-7	breast:
3	chr2:55197790..55202065-chr2:55203128..55206918,7	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000214595	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10173203	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10189094	0.82[EUR][1000 genomes]
rs3198123	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3806572	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7601895	0.82[EUR][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
2	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:55193400-55214800	Strong transcription	HepG2	liver
6	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood
11	chr2:55195000-55215200	Strong transcription	Dnd41	blood
12	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55195200-55205800	Strong transcription	HMEC	breast
14	chr2:55195400-55205200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:55196000-55205800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
20	chr2:55196600-55208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55196800-55204600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:55196800-55204800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:55196800-55205600	Strong transcription	NHEK	skin
26	chr2:55197200-55204800	Strong transcription	K562	blood
27	chr2:55197800-55207800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:55198600-55215200	Weak transcription	Lung	lung
31	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:55199000-55206800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:55199200-55206600	Weak transcription	Hela-S3	cervix
34	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:55199400-55208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55199600-55204800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:55199800-55204600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:55200200-55209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
40	chr2:55200600-55204600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:55200800-55204400	Strong transcription	Brain Germinal Matrix	brain
42	chr2:55200800-55204600	Enhancers	Brain Anterior Caudate	brain
43	chr2:55200800-55208000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
45	chr2:55201000-55204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55201000-55204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:55201000-55208400	Weak transcription	Placenta	Placenta
48	chr2:55201200-55205200	Genic enhancers	HSMM	muscle
49	chr2:55201200-55208000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:55201400-55204200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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