Variant report

Variant	rs10992221
Chromosome Location	chr9:94832043-94832044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94796191..94798036-chr9:94830932..94833373,2	K562	blood:
2	chr9:94822277..94824746-chr9:94829983..94832787,2	K562	blood:
3	chr9:94829684..94833398-chr9:94833829..94839474,7	MCF-7	breast:
4	chr9:94810983..94813724-chr9:94831335..94833078,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10123181	0.88[TSI][hapmap]
rs10820935	0.82[ASN][1000 genomes]
rs10820936	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs10820937	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10820938	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10992212	0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10992215	0.82[ASN][1000 genomes]
rs10992216	0.81[ASN][1000 genomes]
rs10992220	0.81[ASN][1000 genomes]
rs10992222	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10992230	0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10992233	0.84[ASN][1000 genomes]
rs10992234	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs11533009	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12235309	0.81[ASN][1000 genomes]
rs12235310	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12235495	0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12237221	0.82[ASN][1000 genomes]
rs12237598	0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12238682	0.81[ASN][1000 genomes]
rs12337180	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12343974	0.93[ASN][1000 genomes]
rs16908106	0.88[TSI][hapmap]
rs16908135	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs16908137	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1970121	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]
rs28727560	0.83[AMR][1000 genomes]
rs3750440	0.89[CEU][hapmap]
rs3858090	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4518728	0.92[ASN][1000 genomes]
rs58129324	0.84[AMR][1000 genomes]
rs58909848	0.82[ASN][1000 genomes]
rs59183854	0.82[ASN][1000 genomes]
rs59856128	0.82[ASN][1000 genomes]
rs7022553	0.81[ASN][1000 genomes]
rs7029539	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs7046540	0.83[AMR][1000 genomes]
rs7847966	0.96[ASN][1000 genomes]
rs7849220	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7852067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856177	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs7858659	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7860518	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs7862826	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7872238	0.89[ASW][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs7872515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10992221	CDK20	cis	parietal	SCAN
rs10992221	SPTLC1	cis	parietal	SCAN
rs10992221	FANCC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94812200-94832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
4	chr9:94820600-94844400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:94822200-94832600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
7	chr9:94823200-94842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:94823200-94844400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:94823400-94832800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr9:94824000-94843600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr9:94824000-94844000	Strong transcription	Primary B cells from cord blood	blood
12	chr9:94824000-94860400	Weak transcription	Psoas Muscle	Psoas
13	chr9:94824400-94832800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr9:94824800-94844200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:94825000-94833200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:94825200-94833000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr9:94825200-94833000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:94825400-94844200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:94825600-94833200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr9:94825600-94834600	Strong transcription	Dnd41	blood
21	chr9:94825600-94844200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr9:94825600-94844400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr9:94825800-94832600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:94826000-94835000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:94826200-94832800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:94826200-94833000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr9:94826200-94833200	Strong transcription	Fetal Intestine Large	intestine
28	chr9:94826200-94835000	Strong transcription	Adipose Nuclei	Adipose
29	chr9:94826400-94832600	Strong transcription	NHDF-Ad	bronchial
30	chr9:94826400-94835600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:94826400-94843000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:94826600-94833200	Strong transcription	Placenta	Placenta
33	chr9:94826600-94843800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr9:94826800-94832800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:94826800-94833000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:94826800-94844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:94826800-94844400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr9:94826800-94844400	Strong transcription	Primary T cells from cord blood	blood
39	chr9:94827000-94843400	Strong transcription	Thymus	Thymus
40	chr9:94827000-94844000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:94827200-94833200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:94827200-94837400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:94827200-94838400	Strong transcription	GM12878-XiMat	blood
44	chr9:94827200-94856800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:94827400-94832800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:94827400-94836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:94827400-94844000	Strong transcription	Liver	Liver
48	chr9:94827600-94832600	Strong transcription	NH-A	brain
49	chr9:94827800-94833000	Strong transcription	HSMM	muscle
50	chr9:94827800-94843200	Strong transcription	Fetal Stomach	stomach

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