Variant report

Variant	rs16830710
Chromosome Location	chr3:179405728-179405729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179399505..179402257-chr3:179403875..179406189,2	K562	blood:
2	chr3:179369821..179372060-chr3:179405523..179407102,2	MCF-7	breast:
3	chr3:179399505..179402257-chr3:179403875..179406189,3	K562	blood:
4	chr3:179372827..179374690-chr3:179405067..179408048,2	K562	blood:
5	chr3:179380055..179381652-chr3:179404647..179407637,2	K562	blood:

Variant related genes	Relation type
ENSG00000058056	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4854948	0.91[YRI][hapmap]
rs6777944	1.00[TSI][hapmap]
rs73054611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800368	0.81[YRI][hapmap]
rs9811751	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9832389	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	nsv4140	chr3:179383961-179429704	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16830710	NAMPT	trans	brain	seeQTL
rs16830710	CXCL11	trans	brain	seeQTL
rs16830710	SFN	trans	brain	seeQTL
rs16830710	MYBPH	trans	brain	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179372600-179408400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:179372600-179425200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:179374600-179408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:179380600-179418800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:179384400-179410400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:179384800-179406200	Weak transcription	HSMM	muscle
7	chr3:179384800-179408000	Weak transcription	Fetal Thymus	thymus
8	chr3:179384800-179415200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:179384800-179425000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:179384800-179428400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:179384800-179443800	Weak transcription	Esophagus	oesophagus
12	chr3:179385000-179415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:179385000-179439200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:179385000-179448400	Weak transcription	Fetal Brain Male	brain
15	chr3:179385400-179419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:179390800-179408000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:179391000-179444000	Weak transcription	Pancreas	Pancrea
18	chr3:179391000-179452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:179391400-179415400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:179391400-179426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:179391400-179439200	Weak transcription	NHEK	skin
22	chr3:179391600-179408200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:179391600-179412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:179391600-179424000	Weak transcription	Hela-S3	cervix
25	chr3:179392600-179425000	Weak transcription	Aorta	Aorta
26	chr3:179394400-179415600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:179394400-179419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:179396800-179407600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:179397000-179419200	Weak transcription	Liver	Liver
30	chr3:179397200-179423800	Weak transcription	HSMMtube	muscle
31	chr3:179397800-179439200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:179398200-179408400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:179398400-179413600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:179398600-179421800	Weak transcription	Brain Substantia Nigra	brain
35	chr3:179398800-179406400	Weak transcription	Osteobl	bone
36	chr3:179399000-179406400	Weak transcription	NH-A	brain
37	chr3:179399000-179426400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:179399000-179434000	Weak transcription	A549	lung
39	chr3:179399000-179459800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:179399200-179406000	Weak transcription	Spleen	Spleen
41	chr3:179399200-179425000	Weak transcription	Brain Germinal Matrix	brain
42	chr3:179399600-179409800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:179399600-179425000	Weak transcription	Lung	lung
44	chr3:179399800-179409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:179400000-179421600	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:179400000-179424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:179400600-179408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:179400800-179426800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:179401000-179406000	Weak transcription	NHDF-Ad	bronchial
50	chr3:179401000-179406400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links