Variant report

Variant	rs2229994
Chromosome Location	chr5:112178492-112178493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112176097..112178949-chr5:112179046..112180658,2	MCF-7	breast:
2	chr5:112176263..112181367-chr5:112181688..112184725,5	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10477484	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13354540	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1661034	1.00[YRI][hapmap]
rs1697914	1.00[YRI][hapmap]
rs17134945	1.00[CEU][hapmap]
rs2431505	1.00[YRI][hapmap]
rs2431508	1.00[YRI][hapmap]
rs2439592	1.00[YRI][hapmap]
rs2455294	1.00[YRI][hapmap]
rs2464808	1.00[YRI][hapmap]
rs28460815	0.86[EUR][1000 genomes]
rs34083474	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41296563	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61995948	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73220036	0.86[EUR][1000 genomes]
rs7735066	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv965607	chr5:112177487-112179767	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:112152000-112183800	Weak transcription	Gastric	stomach
5	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
9	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:112163400-112183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:112165400-112182400	Weak transcription	Right Ventricle	heart
12	chr5:112168400-112179000	Strong transcription	Fetal Muscle Leg	muscle
13	chr5:112171600-112179600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:112172400-112180000	Strong transcription	Fetal Brain Female	brain
15	chr5:112172600-112179800	Strong transcription	HSMM	muscle
16	chr5:112172800-112179000	Strong transcription	Brain Germinal Matrix	brain
17	chr5:112173200-112179200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:112174000-112182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:112174000-112182400	Weak transcription	Esophagus	oesophagus
20	chr5:112174000-112183800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:112174200-112181200	Weak transcription	Spleen	Spleen
22	chr5:112174200-112183800	Weak transcription	Hela-S3	cervix
23	chr5:112174400-112182400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:112174400-112183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:112174600-112178600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:112174600-112183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:112174600-112184200	Weak transcription	Ovary	ovary
28	chr5:112174800-112179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:112174800-112183800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:112174800-112183800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:112174800-112183800	Weak transcription	NHEK	skin
32	chr5:112175000-112179000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr5:112175200-112183800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:112175400-112183800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:112175400-112187600	Weak transcription	NHLF	lung
36	chr5:112175600-112180200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:112175600-112182200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:112175600-112183800	Weak transcription	Psoas Muscle	Psoas
39	chr5:112175600-112183800	Weak transcription	GM12878-XiMat	blood
40	chr5:112175600-112184000	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:112175600-112184000	Weak transcription	Placenta	Placenta
42	chr5:112175800-112178600	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:112175800-112183600	Weak transcription	Liver	Liver
44	chr5:112175800-112183800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:112175800-112183800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:112175800-112183800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:112175800-112183800	Weak transcription	A549	lung
48	chr5:112175800-112183800	Weak transcription	Dnd41	blood
49	chr5:112176000-112179000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr5:112176000-112181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links