Variant report

Variant	rs7107433
Chromosome Location	chr11:36293048-36293049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C11orf55-2	chr11:36290834-36293377	ENSG00000196559.3

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11033524	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033527	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603166	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12361221	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1562327	0.81[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1900336	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289986	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289987	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4418777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56386213	0.81[EUR][1000 genomes]
rs61878683	0.81[EUR][1000 genomes]
rs61878687	0.87[EUR][1000 genomes]
rs6484831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104737	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7109505	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72946165	0.81[EUR][1000 genomes]
rs7951298	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9667667	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787880	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9787894	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9888212	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9888261	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7107433	SLC1A2	cis	parietal	SCAN
rs7107433	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36276800-36294400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:36278200-36293200	Weak transcription	Fetal Lung	lung
3	chr11:36279200-36294800	Weak transcription	HMEC	breast
4	chr11:36280400-36294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:36280400-36299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:36280800-36300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:36281400-36293200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:36282200-36302000	Weak transcription	NHEK	skin
9	chr11:36283000-36298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:36283200-36300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:36287000-36294200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:36287600-36295400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:36287600-36304800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:36287800-36293400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:36288000-36293200	Weak transcription	Osteobl	bone
16	chr11:36288000-36310200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:36288400-36295200	Weak transcription	NHLF	lung
18	chr11:36288400-36304600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:36289200-36299800	Weak transcription	HepG2	liver
20	chr11:36289200-36300000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:36289400-36293600	Weak transcription	Fetal Kidney	kidney
22	chr11:36289400-36294600	Weak transcription	Fetal Brain Male	brain
23	chr11:36290400-36294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:36290600-36296800	Strong transcription	Fetal Brain Female	brain
25	chr11:36290800-36293200	Weak transcription	Aorta	Aorta
26	chr11:36290800-36310400	Weak transcription	Stomach Mucosa	stomach
27	chr11:36291000-36293400	Weak transcription	HUVEC	blood vessel
28	chr11:36291000-36294200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:36291000-36294400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:36291000-36294600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:36291000-36294600	Strong transcription	Fetal Intestine Small	intestine
32	chr11:36291000-36294800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:36291000-36298200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:36291000-36298400	Strong transcription	Fetal Stomach	stomach
35	chr11:36291000-36301200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:36291000-36301800	Weak transcription	Right Atrium	heart
37	chr11:36291200-36293200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:36291200-36293600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:36291200-36294400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:36291200-36294600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:36291200-36296800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr11:36291200-36298000	Strong transcription	Spleen	Spleen
43	chr11:36291200-36299000	Strong transcription	Adipose Nuclei	Adipose
44	chr11:36291200-36299000	Strong transcription	Ovary	ovary
45	chr11:36291200-36299200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:36291200-36299400	Strong transcription	Brain Angular Gyrus	brain
47	chr11:36291200-36299400	Strong transcription	Brain Hippocampus Middle	brain
48	chr11:36291200-36302200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:36291200-36302400	Strong transcription	Primary T cells from cord blood	blood
50	chr11:36291200-36302800	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links