Variant report

Variant	rs2094054
Chromosome Location	chr13:30508884-30508885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30508008..30510755-chr13:30510923..30512750,2	MCF-7	breast:
2	chr13:30502030..30504176-chr13:30507351..30509428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122043	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs17503208	1.00[AFR][1000 genomes]
rs17503263	1.00[AFR][1000 genomes]
rs17503526	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17503533	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17504027	0.87[AMR][1000 genomes]
rs17587770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17587798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17588071	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17588196	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17588286	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17588314	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17588510	0.87[AMR][1000 genomes]
rs55708888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55734322	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55741316	0.87[AMR][1000 genomes]
rs55772458	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55837941	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55886241	0.82[AMR][1000 genomes]
rs55913576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55922204	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55951457	0.87[AMR][1000 genomes]
rs56077878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56249225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56274510	1.00[AFR][1000 genomes]
rs56275431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56399700	0.87[AMR][1000 genomes]
rs56409314	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73157198	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157199	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73159303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73159304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73159310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73159320	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73159321	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73159339	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73159340	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73159349	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73159358	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73159360	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73159362	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73159365	0.87[AMR][1000 genomes]
rs73159366	0.87[AMR][1000 genomes]
rs73159371	0.87[AMR][1000 genomes]
rs73159389	0.87[AMR][1000 genomes]
rs73159397	0.87[AMR][1000 genomes]
rs73161503	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30499000-30510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr13:30499200-30509000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:30508000-30509400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:30508000-30509400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr13:30508000-30510000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:30508000-30510000	Enhancers	Thymus	Thymus
8	chr13:30508200-30509000	Enhancers	HSMM	muscle
9	chr13:30508200-30509400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr13:30508200-30509800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr13:30508200-30510000	Enhancers	Primary T cells from cord blood	blood
12	chr13:30508200-30510000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr13:30508200-30510000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:30508400-30509400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr13:30508400-30509800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr13:30508400-30509800	Enhancers	Fetal Brain Female	brain
17	chr13:30508400-30510000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr13:30508400-30510000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr13:30508400-30510000	Enhancers	Fetal Thymus	thymus
20	chr13:30508600-30509000	Enhancers	Brain Anterior Caudate	brain
21	chr13:30508600-30509200	Enhancers	Fetal Muscle Leg	muscle
22	chr13:30508600-30509400	Enhancers	GM12878-XiMat	blood
23	chr13:30508600-30509800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr13:30508600-30510400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:30508800-30509000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:30508800-30509800	Enhancers	Brain Cingulate Gyrus	brain
27	chr13:30508800-30510600	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links