Variant report

Variant	rs16971454
Chromosome Location	chr15:41361138-41361139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11852419	1.00[ASN][1000 genomes]
rs11855854	1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs17659661	1.00[CHB][hapmap]
rs17715742	1.00[CHB][hapmap]
rs28516832	1.00[ASN][1000 genomes]
rs28538451	1.00[ASN][1000 genomes]
rs28551767	1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs513280	1.00[CHB][hapmap]
rs522063	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv974711	chr15:41360002-41370961	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16971454	TTBK2	cis	cerebellum	SCAN
rs16971454	NDUFAF1	cis	lymphoblastoid	seeQTL
rs16971454	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs16971454	NUSAP1	cis	cerebellum	SCAN
rs16971454	GPR176	cis	parietal	SCAN
rs16971454	NDUFAF1	cis	parietal	SCAN
rs16971454	IVD	cis	cerebellum	SCAN
rs16971454	NUSAP1	cis	brain	BrainEAC
rs16971454	MGA	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:41336800-41380400	Strong transcription	Osteobl	bone
4	chr15:41340800-41366800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:41341600-41389000	Strong transcription	Liver	Liver
6	chr15:41345200-41373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:41346800-41368600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:41347000-41380200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:41348400-41363400	Strong transcription	Brain Germinal Matrix	brain
10	chr15:41349400-41362400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:41349400-41365200	Weak transcription	Fetal Heart	heart
12	chr15:41351200-41363800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:41354000-41368600	Strong transcription	NH-A	brain
14	chr15:41354200-41389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:41354600-41367400	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr15:41354600-41388800	Strong transcription	Fetal Intestine Large	intestine
17	chr15:41354600-41389000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr15:41354800-41388600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr15:41354800-41389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:41355000-41361600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:41355000-41361600	Weak transcription	HMEC	breast
22	chr15:41355000-41362000	Strong transcription	Fetal Intestine Small	intestine
23	chr15:41355000-41363400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:41355000-41364400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:41355000-41364400	Strong transcription	Left Ventricle	heart
26	chr15:41355000-41367200	Strong transcription	Ovary	ovary
27	chr15:41355000-41367400	Strong transcription	Adipose Nuclei	Adipose
28	chr15:41355000-41369200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:41355000-41370800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr15:41355000-41374200	Strong transcription	Hela-S3	cervix
31	chr15:41355000-41380200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:41355000-41380800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:41355000-41381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:41355000-41388400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
36	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
37	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:41355200-41367200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr15:41355200-41370600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:41355200-41388600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:41355200-41388800	Strong transcription	Primary T cells from cord blood	blood
43	chr15:41355400-41362000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:41355400-41362400	Weak transcription	Colonic Mucosa	Colon
45	chr15:41355400-41362600	Weak transcription	Small Intestine	intestine
46	chr15:41355400-41368800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:41355400-41369000	Strong transcription	Thymus	Thymus
48	chr15:41355400-41369200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:41355400-41370800	Weak transcription	Pancreas	Pancrea
50	chr15:41355400-41371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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