Variant report

Variant	rs11861296
Chromosome Location	chr16:71850632-71850633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71842412..71844852-chr16:71850113..71852439,2	MCF-7	breast:
2	chr16:71842099..71845312-chr16:71845371..71851524,8	K562	blood:
3	chr16:71842293..71844591-chr16:71850006..71852078,2	K562	blood:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10500560	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs10500567	0.82[JPT][hapmap]
rs10852505	1.00[JPT][hapmap]
rs11075903	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11641113	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11642529	0.82[GIH][hapmap];0.86[ASN][1000 genomes]
rs11644740	0.82[JPT][hapmap]
rs11645704	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11645725	0.86[EUR][1000 genomes]
rs11648557	0.82[JPT][hapmap]
rs11865456	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs12149307	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12149325	0.82[JPT][hapmap]
rs12149460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445564	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12445641	0.82[ASW][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12446005	0.96[GIH][hapmap];0.83[TSI][hapmap]
rs12447094	0.85[EUR][1000 genomes]
rs12448022	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12919271	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12928939	0.86[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12933007	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12934512	0.82[JPT][hapmap]
rs12935106	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1345868	0.96[GIH][hapmap];0.83[TSI][hapmap]
rs17357420	0.96[GIH][hapmap];0.82[JPT][hapmap]
rs17358402	0.82[JPT][hapmap]
rs28667298	0.80[EUR][1000 genomes]
rs2878494	1.00[JPT][hapmap]
rs34053338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34531032	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34680964	0.96[GIH][hapmap];0.83[TSI][hapmap]
rs34998650	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3751820	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs4528577	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs71386932	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7185027	0.82[ASN][1000 genomes]
rs7188591	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7195988	0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs7197104	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7197486	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7198834	0.96[GIH][hapmap];0.82[JPT][hapmap]
rs7200447	0.83[EUR][1000 genomes]
rs7202840	0.86[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8049163	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs8050058	0.96[GIH][hapmap];0.82[JPT][hapmap]
rs8051878	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8052358	0.96[GIH][hapmap];0.82[JPT][hapmap]
rs8057568	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9932707	0.82[JPT][hapmap]
rs9939911	0.82[JPT][hapmap]
rs9940234	0.82[GIH][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11861296	NRN1L	cis	parietal	SCAN
rs11861296	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71843600-71852600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:71843800-71850800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:71843800-71850800	Weak transcription	HSMM	muscle
4	chr16:71843800-71851600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr16:71843800-71851600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr16:71843800-71855400	Weak transcription	Primary T cells from cord blood	blood
7	chr16:71843800-71861600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:71844000-71859400	Weak transcription	Fetal Intestine Small	intestine
9	chr16:71844200-71862200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:71844800-71862000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr16:71845200-71851800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:71845600-71851600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:71846600-71851600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:71848600-71852200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:71849400-71851800	Enhancers	NHLF	lung
16	chr16:71849600-71850800	Enhancers	GM12878-XiMat	blood
17	chr16:71849800-71851800	Enhancers	NHDF-Ad	bronchial
18	chr16:71850000-71850800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:71850000-71851000	Enhancers	Colon Smooth Muscle	Colon
20	chr16:71850000-71851600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:71850000-71851800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr16:71850200-71851200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr16:71850200-71852000	Enhancers	Primary B cells from peripheral blood	blood
24	chr16:71850200-71852200	Enhancers	Placenta	Placenta
25	chr16:71850400-71850800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr16:71850400-71851000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr16:71850400-71851000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr16:71850400-71851200	Enhancers	Fetal Stomach	stomach
29	chr16:71850400-71851200	Enhancers	HUVEC	blood vessel
30	chr16:71850400-71851400	Enhancers	Fetal Muscle Trunk	muscle
31	chr16:71850400-71851800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr16:71850400-71851800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr16:71850400-71852200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:71850400-71852200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr16:71850600-71850800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:71850600-71850800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr16:71850600-71850800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:71850600-71850800	Enhancers	Brain Anterior Caudate	brain
39	chr16:71850600-71850800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr16:71850600-71850800	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr16:71850600-71850800	Enhancers	NHEK	skin
42	chr16:71850600-71851000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:71850600-71851000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr16:71850600-71851000	Enhancers	Brain Angular Gyrus	brain
45	chr16:71850600-71851000	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr16:71850600-71851000	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr16:71850600-71851000	Flanking Active TSS	A549	lung
48	chr16:71850600-71851000	Enhancers	K562	blood
49	chr16:71850600-71851000	Active TSS	Osteobl	bone
50	chr16:71850600-71851200	Flanking Active TSS	Hela-S3	cervix

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