Variant report

Variant	rs2649656
Chromosome Location	chr11:57320350-57320351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57318967..57320703-chr11:57326356..57328745,2	MCF-7	breast:
2	chr11:57320019..57321900-chr11:57327582..57330146,3	K562	blood:
3	chr11:57319867..57321900-chr11:57327404..57329278,2	K562	blood:

Variant related genes	Relation type
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1124942	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223229	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234409	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2467328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2467329	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467330	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581930	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2649644	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649645	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649653	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2649655	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649658	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649666	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729358	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729359	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729360	0.95[JPT][hapmap]
rs2729367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729368	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729369	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729370	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729373	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729375	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848621	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2848624	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848638	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514385	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5847	0.95[JPT][hapmap]
rs722823	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2649656	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2649656	SMTNL1	cis	lung	GTEx
rs2649656	SMTNL1	cis	Nerve Tibial	GTEx
rs2649656	OR5J2	cis	parietal	SCAN
rs2649656	UBE2L6	cis	parietal	SCAN
rs2649656	SMTNL1	cis	Artery Tibial	GTEx
rs2649656	SMTNL1	cis	lymphoblastoid	seeQTL
rs2649656	SLC43A3	cis	cerebellum	SCAN
rs2649656	DTX4	cis	cerebellum	SCAN
rs2649656	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs2649656	SMTNL1	cis	Thyroid	GTEx
rs2649656	SLC43A1	cis	parietal	SCAN
rs2649656	SMTNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2649656	SMTNL1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
2	chr11:57307200-57333600	Weak transcription	HMEC	breast
3	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
4	chr11:57311400-57320400	Weak transcription	Stomach Mucosa	stomach
5	chr11:57313000-57326800	Strong transcription	Thymus	Thymus
6	chr11:57313200-57327600	Strong transcription	Fetal Brain Female	brain
7	chr11:57313200-57330000	Strong transcription	Dnd41	blood
8	chr11:57313400-57327800	Strong transcription	Brain Germinal Matrix	brain
9	chr11:57313400-57328000	Strong transcription	Fetal Stomach	stomach
10	chr11:57313600-57323000	Strong transcription	Liver	Liver
11	chr11:57313600-57327800	Strong transcription	Fetal Thymus	thymus
12	chr11:57313600-57328600	Strong transcription	Lung	lung
13	chr11:57314000-57326600	Strong transcription	Brain Anterior Caudate	brain
14	chr11:57314000-57328000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:57314000-57328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:57314000-57328600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:57314000-57330200	Strong transcription	Fetal Intestine Small	intestine
18	chr11:57314000-57330400	Strong transcription	Primary T cells from cord blood	blood
19	chr11:57314200-57321400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:57314200-57323800	Strong transcription	Brain Hippocampus Middle	brain
21	chr11:57314200-57326400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:57314200-57329800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:57314400-57326600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:57314600-57328000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:57314800-57327200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:57314800-57330600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:57315000-57328000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:57315000-57330000	Weak transcription	NHEK	skin
29	chr11:57315200-57323400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:57315200-57328000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:57315200-57328000	Strong transcription	Fetal Intestine Large	intestine
32	chr11:57315200-57329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:57315200-57329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:57315200-57330600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:57315400-57329000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:57315600-57330600	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:57315800-57322800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:57315800-57327600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:57315800-57327800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:57315800-57327800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr11:57315800-57328000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:57315800-57328200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:57315800-57330000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:57315800-57330200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr11:57315800-57330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:57316000-57321600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:57316000-57328000	Strong transcription	GM12878-XiMat	blood
48	chr11:57316200-57322200	Strong transcription	Esophagus	oesophagus
49	chr11:57316200-57328000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:57316200-57328000	Strong transcription	Stomach Smooth Muscle	stomach

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