Variant report

Variant	rs16876519
Chromosome Location	chr6:15496122-15496123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15494495..15496719-chr6:15502901..15504506,2	K562	blood:
2	chr6:15211347..15213015-chr6:15495121..15498048,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11753594	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11756854	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11756950	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11758484	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11759250	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11759978	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2327897	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2876393	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41267698	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55862621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55901822	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56070118	0.84[EUR][1000 genomes]
rs56381700	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58121172	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72836316	0.85[EUR][1000 genomes]
rs72836347	0.86[EUR][1000 genomes]
rs72837821	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72837824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16876519	NHLRC1	cis	parietal	SCAN
rs16876519	RBM24	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15471000-15502000	Weak transcription	A549	lung
2	chr6:15484800-15496400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:15486800-15502000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:15489200-15496200	Weak transcription	Small Intestine	intestine
6	chr6:15489200-15496800	Weak transcription	Colonic Mucosa	Colon
7	chr6:15489200-15504400	Weak transcription	Fetal Brain Female	brain
8	chr6:15490000-15496200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:15490000-15496400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:15490200-15496400	Weak transcription	Gastric	stomach
11	chr6:15490200-15496400	Weak transcription	Pancreas	Pancrea
12	chr6:15490800-15496800	Enhancers	HSMMtube	muscle
13	chr6:15491400-15496200	Enhancers	Ovary	ovary
14	chr6:15491800-15501400	Weak transcription	NH-A	brain
15	chr6:15492000-15496800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:15492000-15498400	Weak transcription	Stomach Mucosa	stomach
17	chr6:15492000-15501800	Weak transcription	Fetal Brain Male	brain
18	chr6:15492200-15501200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:15492200-15507800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:15492200-15508200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:15492200-15527000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:15492400-15496200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:15492400-15496400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:15492400-15496400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:15492400-15498600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:15492400-15502400	Strong transcription	Fetal Intestine Small	intestine
27	chr6:15492400-15527200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:15492600-15496200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:15492600-15522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:15492800-15515000	Strong transcription	Thymus	Thymus
31	chr6:15492800-15527000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:15493000-15501600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:15493000-15501600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:15493000-15501800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:15493000-15504200	Strong transcription	Fetal Thymus	thymus
36	chr6:15493400-15502000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:15493600-15496200	Weak transcription	Fetal Intestine Large	intestine
38	chr6:15493800-15497000	Weak transcription	GM12878-XiMat	blood
39	chr6:15493800-15520000	Weak transcription	Hela-S3	cervix
40	chr6:15494000-15496400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:15494200-15496200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:15494200-15496400	Weak transcription	Brain Germinal Matrix	brain
43	chr6:15494200-15496400	Genic enhancers	Fetal Stomach	stomach
44	chr6:15494200-15522400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr6:15494400-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:15494400-15501600	Weak transcription	Fetal Kidney	kidney
47	chr6:15494600-15496400	Weak transcription	NHLF	lung
48	chr6:15494600-15506000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:15494600-15507400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:15494800-15496600	Enhancers	Skeletal Muscle Female	skeletal muscle

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