Variant report

Variant	rs11604616
Chromosome Location	chr11:9157925-9157926
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9108004..9116385-chr11:9156452..9162678,21	MCF-7	breast:
2	chr11:9109700..9116224-chr11:9155740..9163743,14	MCF-7	breast:
3	chr11:9104308..9106078-chr11:9156890..9159293,2	MCF-7	breast:
4	chr11:9041862..9044730-chr11:9157486..9160225,2	MCF-7	breast:
5	chr11:9023067..9025427-chr11:9156418..9158861,2	K562	blood:

Variant related genes	Relation type
ENSG00000175356	Chromatin interaction
ENSG00000213538	Chromatin interaction
ENSG00000264984	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10047438	0.88[ASN][1000 genomes]
rs1039210	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10769991	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769992	0.83[JPT][hapmap]
rs10769993	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769995	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769996	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840174	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10840176	0.98[ASN][1000 genomes]
rs10840178	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840179	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840181	0.81[ASN][1000 genomes]
rs10840182	0.81[ASN][1000 genomes]
rs10840183	0.88[ASN][1000 genomes]
rs10840185	0.83[ASN][1000 genomes]
rs11042195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042199	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1353730	0.92[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17256375	0.82[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1874822	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1997628	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2133217	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2291839	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2647537	0.92[JPT][hapmap]
rs2742556	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2742557	0.84[ASN][1000 genomes]
rs3898554	0.91[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4910035	0.84[ASN][1000 genomes]
rs56077948	0.81[ASN][1000 genomes]
rs56216908	0.91[ASN][1000 genomes]
rs7109745	0.85[ASN][1000 genomes]
rs7123970	0.87[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7128469	0.83[ASN][1000 genomes]
rs7395347	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7395846	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7947251	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7948219	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9888257	0.92[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11604616	OR10A6	cis	cerebellum	SCAN
rs11604616	TMEM41B	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9134800-9159000	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:9134800-9161200	Weak transcription	Fetal Brain Male	brain
4	chr11:9136400-9159200	Weak transcription	Brain Anterior Caudate	brain
5	chr11:9137200-9159000	Weak transcription	Fetal Heart	heart
6	chr11:9141600-9158400	Weak transcription	Pancreas	Pancrea
7	chr11:9142400-9163000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:9142600-9159000	Weak transcription	Adipose Nuclei	Adipose
9	chr11:9142600-9159200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:9142600-9175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:9143400-9159200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:9143400-9161200	Weak transcription	Aorta	Aorta
13	chr11:9143600-9159000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:9143800-9158800	Weak transcription	Fetal Brain Female	brain
15	chr11:9144400-9161200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:9146400-9158400	Weak transcription	Gastric	stomach
17	chr11:9146400-9159200	Weak transcription	K562	blood
18	chr11:9146600-9158800	Weak transcription	Lung	lung
19	chr11:9147000-9158800	Weak transcription	A549	lung
20	chr11:9148400-9158400	Weak transcription	GM12878-XiMat	blood
21	chr11:9148400-9159000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:9148400-9159000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:9148400-9159200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:9148600-9159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:9148800-9158000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:9148800-9159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:9149000-9158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:9150600-9160000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:9151600-9158400	Weak transcription	HSMMtube	muscle
30	chr11:9151800-9159000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:9151800-9160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:9151800-9175800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:9152000-9158800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:9152000-9159800	Weak transcription	Liver	Liver
35	chr11:9152200-9160600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:9152400-9158400	Weak transcription	Thymus	Thymus
37	chr11:9152400-9159000	Weak transcription	Fetal Intestine Small	intestine
38	chr11:9152400-9159000	Weak transcription	Hela-S3	cervix
39	chr11:9152600-9158400	Weak transcription	Fetal Thymus	thymus
40	chr11:9152600-9158800	Weak transcription	Fetal Lung	lung
41	chr11:9152600-9159000	Weak transcription	HepG2	liver
42	chr11:9152600-9160200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:9152800-9159000	Weak transcription	Fetal Intestine Large	intestine
44	chr11:9152800-9159000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:9152800-9159600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:9152800-9175800	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:9153000-9159000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:9153000-9159600	Weak transcription	Spleen	Spleen
49	chr11:9153000-9160200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:9153000-9179800	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links