Variant report

Variant	rs17787217
Chromosome Location	chr3:23907775-23907776
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	chr3:23850663..23852864-chr3:23907754..23910540,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11129127	0.82[AMR][1000 genomes]
rs1139150	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11918791	0.88[ASN][1000 genomes]
rs13085379	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13094627	0.94[ASN][1000 genomes]
rs2885034	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34963628	0.84[AMR][1000 genomes]
rs34986000	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4538321	0.94[ASN][1000 genomes]
rs6550805	0.85[CHB][hapmap]
rs6779573	0.85[CHB][hapmap]
rs6798386	0.85[AMR][1000 genomes]
rs73034778	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619342	0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9990089	0.89[ASN][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17787217	NKIRAS1	cis	parietal	SCAN
rs17787217	NKIRAS1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23901200-23914800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:23901200-23915400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23901200-23915400	Weak transcription	HSMM	muscle
4	chr3:23901200-23942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:23901400-23915200	Weak transcription	NHEK	skin
6	chr3:23901800-23928800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:23901800-23935600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:23903400-23929400	Weak transcription	Dnd41	blood
9	chr3:23903600-23908200	Enhancers	Hela-S3	cervix
10	chr3:23904000-23918200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:23904200-23908200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:23904800-23930800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:23905200-23909600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:23905400-23907800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:23905400-23909600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:23905400-23909600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:23905600-23908000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:23905600-23908200	Enhancers	Liver	Liver
19	chr3:23905600-23908200	Enhancers	Brain Hippocampus Middle	brain
20	chr3:23905600-23908400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:23905600-23908400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:23905600-23909200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:23905600-23909200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:23905800-23909200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:23906000-23908200	Enhancers	HepG2	liver
26	chr3:23906000-23908200	Enhancers	NHLF	lung
27	chr3:23906200-23907800	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:23906200-23908000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:23906200-23908000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:23906200-23908000	Genic enhancers	Fetal Intestine Small	intestine
31	chr3:23906200-23908000	Enhancers	Fetal Muscle Leg	muscle
32	chr3:23906200-23908000	Enhancers	Left Ventricle	heart
33	chr3:23906200-23908000	Enhancers	Ovary	ovary
34	chr3:23906200-23908000	Enhancers	Right Atrium	heart
35	chr3:23906200-23908200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:23906200-23908400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:23906200-23908400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:23906200-23908400	Enhancers	Fetal Lung	lung
39	chr3:23906200-23908400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:23906200-23908600	Enhancers	Brain Anterior Caudate	brain
41	chr3:23906200-23909400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr3:23906400-23908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:23906400-23908000	Enhancers	Aorta	Aorta
44	chr3:23906400-23908000	Enhancers	Gastric	stomach
45	chr3:23906400-23908200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:23906400-23908200	Enhancers	Adipose Nuclei	Adipose
47	chr3:23906400-23908200	Enhancers	Brain Angular Gyrus	brain
48	chr3:23906400-23908200	Enhancers	Brain Substantia Nigra	brain
49	chr3:23906400-23908200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:23906400-23908200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links