Variant report

Variant	rs1472399
Chromosome Location	chr4:77886046-77886047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77883715..77886420-chr4:77899296..77901087,2	K562	blood:
2	chr4:77884853..77887082-chr4:77888550..77891018,2	MCF-7	breast:
3	chr4:77868648..77873147-chr4:77883433..77888727,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138758	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10002443	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10006033	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10470896	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10856952	1.00[GIH][hapmap]
rs11559161	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17002332	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17002334	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17002346	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2279711	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2645668	1.00[GIH][hapmap]
rs4252773	1.00[GIH][hapmap]
rs4252896	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4557282	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6817626	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6824360	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7667891	1.00[GIH][hapmap];1.00[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1810313	chr4:77778670-77902099	Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77872600-77890800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:77872600-77894400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:77872600-77899200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:77872600-77900400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:77873000-77899200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:77873400-77894200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:77873400-77894400	Weak transcription	NHEK	skin
8	chr4:77874400-77891000	Weak transcription	K562	blood
9	chr4:77876000-77887200	Weak transcription	HMEC	breast
10	chr4:77876000-77895200	Weak transcription	Aorta	Aorta
11	chr4:77876400-77891200	Weak transcription	HUVEC	blood vessel
12	chr4:77876600-77887200	Weak transcription	Psoas Muscle	Psoas
13	chr4:77876600-77895400	Weak transcription	Right Atrium	heart
14	chr4:77876800-77906000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:77877800-77890400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:77878000-77890400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:77878400-77890600	Weak transcription	Ovary	ovary
18	chr4:77878600-77888200	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:77878800-77899200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:77879000-77893600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:77879000-77894400	Weak transcription	Fetal Stomach	stomach
22	chr4:77879000-77898400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:77879600-77893400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:77879600-77894200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:77879600-77904200	Weak transcription	Gastric	stomach
26	chr4:77881200-77889800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:77881600-77891200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:77881600-77899200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:77881800-77889800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:77882200-77893000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:77882200-77905200	Weak transcription	Fetal Intestine Large	intestine
32	chr4:77882400-77893400	Weak transcription	NH-A	brain
33	chr4:77883800-77888800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:77884000-77891200	Weak transcription	Brain Germinal Matrix	brain
35	chr4:77884200-77886400	ZNF genes & repeats	GM12878-XiMat	blood
36	chr4:77884200-77891000	Weak transcription	Fetal Brain Female	brain
37	chr4:77884200-77893200	Weak transcription	NHLF	lung
38	chr4:77884200-77894400	Weak transcription	Fetal Intestine Small	intestine
39	chr4:77884400-77886200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:77884600-77886600	Strong transcription	HSMM	muscle
41	chr4:77884600-77886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:77884600-77890000	Weak transcription	Fetal Kidney	kidney
43	chr4:77884600-77893200	Weak transcription	Fetal Brain Male	brain
44	chr4:77884600-77893600	Weak transcription	Fetal Lung	lung
45	chr4:77884800-77886200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:77884800-77893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:77884800-77899200	Weak transcription	Placenta	Placenta
48	chr4:77884800-77899200	Weak transcription	Small Intestine	intestine
49	chr4:77884800-77904200	Weak transcription	Pancreas	Pancrea
50	chr4:77885400-77886200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links