Variant report

Variant	rs16911887
Chromosome Location	chr9:97734605-97734606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97686185..97688613-chr9:97732674..97735210,2	MCF-7	breast:
2	chr9:97733399..97735846-chr9:97769206..97770842,2	MCF-7	breast:
3	chr9:97734273..97736580-chr9:97765840..97768486,2	MCF-7	breast:
4	chr9:97731595..97733537-chr9:97733949..97736819,2	MCF-7	breast:
5	chr9:97733013..97735373-chr9:97738780..97740333,2	MCF-7	breast:
6	chr9:97711689..97714649-chr9:97733547..97735329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10512250	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993358	1.00[GIH][hapmap]
rs10993359	0.86[GIH][hapmap]
rs10993371	1.00[GIH][hapmap]
rs10993409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993422	1.00[ASW][hapmap];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993428	1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993429	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993432	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993437	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993438	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993440	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993447	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993450	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236203	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16911884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911886	0.90[CHB][hapmap]
rs3802457	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802458	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56855628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57054200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58325577	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59246309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59630616	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023719	0.85[JPT][hapmap]
rs7848018	0.90[CHB][hapmap];1.00[TSI][hapmap]
rs7857726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866661	0.90[CHB][hapmap];1.00[TSI][hapmap]
rs7867908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875287	0.86[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875888	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16911887	SCGB2A2	trans	brain	seeQTL
rs16911887	SCGB1D2	trans	brain	seeQTL
rs16911887	C2CD4B	trans	brain	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
3	chr9:97714200-97735800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:97715000-97735600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
6	chr9:97715200-97748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:97715400-97735800	Weak transcription	Right Ventricle	heart
8	chr9:97715400-97741200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
10	chr9:97715600-97742000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:97715600-97742000	Weak transcription	Psoas Muscle	Psoas
12	chr9:97715600-97742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:97715800-97735600	Weak transcription	NHDF-Ad	bronchial
14	chr9:97716000-97735200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:97716000-97742400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:97716200-97735200	Weak transcription	NH-A	brain
17	chr9:97716200-97735400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:97716600-97735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:97718800-97736800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:97718800-97744000	Weak transcription	GM12878-XiMat	blood
21	chr9:97719000-97735600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:97719000-97735800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:97719000-97743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:97719000-97745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:97719400-97735400	Weak transcription	Osteobl	bone
26	chr9:97719400-97735600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:97719400-97735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:97719400-97737800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:97719400-97739800	Weak transcription	Primary T cells from cord blood	blood
30	chr9:97719400-97746200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:97719400-97747000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:97719600-97747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:97720800-97741600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:97724800-97743000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:97724800-97743000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:97726800-97742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:97728000-97735600	Weak transcription	Brain Anterior Caudate	brain
38	chr9:97728000-97742800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:97728000-97754200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:97728200-97741400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:97730000-97737400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:97731600-97743000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:97732000-97738000	Enhancers	HepG2	liver
44	chr9:97732200-97734800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:97732200-97735200	Enhancers	Ovary	ovary
46	chr9:97732600-97734800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr9:97732600-97739800	Enhancers	Fetal Intestine Large	intestine
48	chr9:97732800-97742400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:97733400-97735400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:97733400-97736200	Enhancers	Pancreas	Pancrea

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