Variant report

Variant	rs173396
Chromosome Location	chr11:9759918-9759919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9759666..9763532-chr11:9766394..9768623,4	K562	blood:
2	chr11:9759666..9763371-chr11:9766657..9768623,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1032550	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10743117	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743118	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840293	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10840294	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840295	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840296	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840305	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs10840306	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12360647	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12788348	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1996794	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2649044	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs360136	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360137	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360139	0.86[ASN][1000 genomes]
rs360153	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360155	0.95[EUR][1000 genomes]
rs360156	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360157	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360158	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs373894	0.94[ASN][1000 genomes]
rs3751000	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs378825	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs415895	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs429835	0.83[JPT][hapmap]
rs472109	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910063	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4910498	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4910499	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs491205	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7126913	0.91[JPT][hapmap]
rs93138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs93139	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943599	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs173396	MRVI1	cis	parietal	SCAN
rs173396	ASCL3	cis	parietal	SCAN
rs173396	OR52E8	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9733600-9761600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9740000-9762000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:9742200-9779400	Weak transcription	Fetal Brain Male	brain
4	chr11:9744600-9761400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:9745000-9775600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:9749000-9761800	Weak transcription	Small Intestine	intestine
7	chr11:9749000-9764400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:9749000-9764400	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr11:9749400-9764400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:9749600-9764400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:9751000-9764400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:9753800-9764400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:9754000-9764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:9754200-9764400	Strong transcription	Adipose Nuclei	Adipose
15	chr11:9754400-9761600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:9754400-9764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:9754800-9764400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:9755000-9761200	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:9755000-9761400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:9755000-9761600	Weak transcription	Brain Hippocampus Middle	brain
21	chr11:9755000-9761800	Weak transcription	Right Ventricle	heart
22	chr11:9755000-9777600	Weak transcription	Colonic Mucosa	Colon
23	chr11:9755400-9760800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:9755400-9761600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:9755400-9769800	Weak transcription	Pancreas	Pancrea
26	chr11:9756600-9762800	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr11:9756600-9764400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:9756800-9762400	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:9756800-9764400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:9756800-9764400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:9757000-9762600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:9757200-9760200	Genic enhancers	HUVEC	blood vessel
33	chr11:9757200-9760600	Genic enhancers	Placenta	Placenta
34	chr11:9757400-9760400	Genic enhancers	Primary B cells from cord blood	blood
35	chr11:9757400-9760600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:9757400-9761400	Weak transcription	NH-A	brain
37	chr11:9757400-9761600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:9757400-9764600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:9757400-9766400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:9757400-9769200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr11:9757600-9763600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:9757600-9774600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:9757800-9760400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:9757800-9760400	Weak transcription	Osteobl	bone
45	chr11:9757800-9761800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:9757800-9764400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:9757800-9764400	Strong transcription	Fetal Stomach	stomach
48	chr11:9758000-9761800	Genic enhancers	Fetal Thymus	thymus
49	chr11:9758000-9763200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:9758000-9763600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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