Variant report

Variant	rs16912622
Chromosome Location	chr9:100843660-100843661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100842983..100846250-chr9:100851999..100855804,4	MCF-7	breast:
2	chr9:100842838..100844707-chr9:100881208..100883358,2	MCF-7	breast:
3	chr9:100842880..100846056-chr9:100849764..100852020,3	MCF-7	breast:
4	chr9:100842559..100845315-chr9:101012488..101014157,2	MCF-7	breast:
5	chr9:100842650..100845592-chr9:100845952..100848847,2	MCF-7	breast:
6	chr9:100684598..100687225-chr9:100842105..100844747,2	K562	blood:
7	chr9:100817966..100819958-chr9:100840027..100843917,3	K562	blood:
8	chr9:100843269..100846185-chr9:100848032..100850204,2	K562	blood:
9	chr9:100842280..100844769-chr9:100879230..100881771,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1059273	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10985065	0.82[JPT][hapmap]
rs12001675	0.80[CEU][hapmap]
rs12552242	0.82[JPT][hapmap]
rs12554172	0.80[CEU][hapmap]
rs12554583	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2224773	0.84[ASN][1000 genomes]
rs2281732	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739670	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3739672	0.82[GIH][hapmap]
rs3780471	0.83[TSI][hapmap]
rs4300105	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4394518	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4562446	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742711	0.80[CEU][hapmap]
rs4742716	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743150	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs4743157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743159	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55978131	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58427887	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478539	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6478556	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478563	0.82[JPT][hapmap]
rs7020081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7022455	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs7034147	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7038592	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041811	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7046514	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7846772	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7846880	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7848430	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850685	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs7855251	0.82[JPT][hapmap]
rs7862535	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867404	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7869762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs874610	0.80[CEU][hapmap];0.81[GIH][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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040483	chr9:100835325-100868437	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16912622	NANS	cis	parietal	SCAN
rs16912622	C9orf156	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100819600-100848400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100820000-100847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:100820000-100849600	Weak transcription	Fetal Brain Male	brain
4	chr9:100820000-100850000	Weak transcription	Fetal Kidney	kidney
5	chr9:100821200-100849600	Weak transcription	Right Atrium	heart
6	chr9:100837200-100844400	Weak transcription	Psoas Muscle	Psoas
7	chr9:100837400-100845200	Strong transcription	K562	blood
8	chr9:100838200-100852800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:100838600-100848400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:100838600-100852000	Strong transcription	GM12878-XiMat	blood
11	chr9:100839000-100845000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr9:100839000-100848400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:100839000-100849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:100839000-100849800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:100839200-100847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:100839400-100847600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:100839400-100847800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr9:100839400-100848600	Strong transcription	Fetal Stomach	stomach
19	chr9:100839400-100850400	Strong transcription	Dnd41	blood
20	chr9:100839400-100861800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:100839600-100849400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:100839600-100850600	Strong transcription	Thymus	Thymus
23	chr9:100839800-100845200	Strong transcription	Adipose Nuclei	Adipose
24	chr9:100839800-100847400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:100840000-100845000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:100840000-100845400	Strong transcription	Spleen	Spleen
27	chr9:100840000-100846000	Strong transcription	Rectal Smooth Muscle	rectum
28	chr9:100840000-100846400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:100840000-100846600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:100840000-100846800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:100840000-100847000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr9:100840000-100847800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:100840400-100844000	Strong transcription	Brain Anterior Caudate	brain
34	chr9:100840800-100844400	Weak transcription	Small Intestine	intestine
35	chr9:100841200-100846000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:100841600-100848200	Strong transcription	Primary T cells from cord blood	blood
37	chr9:100841800-100845400	Strong transcription	Fetal Muscle Leg	muscle
38	chr9:100841800-100845600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:100841800-100846400	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:100842000-100844200	Genic enhancers	Esophagus	oesophagus
41	chr9:100842000-100845600	Genic enhancers	Placenta	Placenta
42	chr9:100842000-100845800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:100842000-100845800	Genic enhancers	HSMMtube	muscle
44	chr9:100842000-100846200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr9:100842000-100846200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr9:100842000-100847600	Strong transcription	Left Ventricle	heart
47	chr9:100842200-100844000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:100842400-100846800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr9:100842400-100849800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:100842600-100844000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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