Variant report

Variant	rs11357
Chromosome Location	chr2:55470115-55470116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55469201..55471074-chr2:55473270..55475726,2	K562	blood:
2	chr2:55468640..55470171-chr2:55482025..55483624,2	MCF-7	breast:
3	chr2:55468652..55470899-chr2:55494882..55496931,2	MCF-7	breast:
4	chr11:120172949..120175534-chr2:55468115..55470994,2	MCF-7	breast:
5	chr2:55468207..55471857-chr2:55475862..55479587,5	K562	blood:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10193886	0.84[YRI][hapmap]
rs10200120	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200424	0.84[YRI][hapmap]
rs1056445	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052613	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12988617	0.84[ASN][1000 genomes]
rs1437393	0.86[YRI][hapmap]
rs2576711	0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2576712	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576719	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576721	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2589080	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589092	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589093	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589094	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2589096	0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs2589100	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864819	0.90[ASN][1000 genomes]
rs2864826	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920967	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34348115	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs34511570	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4435493	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs55997390	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56039135	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6545477	0.82[YRI][hapmap]
rs6545480	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6706815	0.81[ASN][1000 genomes]
rs6711753	0.82[YRI][hapmap]
rs6727118	0.85[YRI][hapmap]
rs6727131	0.82[YRI][hapmap]
rs6737227	1.00[JPT][hapmap]
rs6747364	0.82[YRI][hapmap]
rs6755515	0.86[ASN][1000 genomes]
rs72799507	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7580936	0.84[EUR][1000 genomes]
rs7597293	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs934709	0.80[CHB][hapmap]
rs9677948	0.82[YRI][hapmap]

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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11357	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs11357	CLHC1	cis	Artery Tibial	GTEx
rs11357	CLHC1	cis	Adipose Subcutaneous	GTEx
rs11357	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
5	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
6	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
8	chr2:55461800-55472400	Weak transcription	Gastric	stomach
9	chr2:55461800-55472400	Weak transcription	Right Ventricle	heart
10	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
13	chr2:55462000-55472600	Weak transcription	Fetal Heart	heart
14	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:55462200-55473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
17	chr2:55462400-55476800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55462400-55476800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:55463200-55470400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:55463400-55470400	Strong transcription	Osteobl	bone
27	chr2:55463400-55472400	Weak transcription	Lung	lung
28	chr2:55463400-55472400	Weak transcription	Ovary	ovary
29	chr2:55463400-55474200	Weak transcription	Aorta	Aorta
30	chr2:55463400-55475800	Weak transcription	Spleen	Spleen
31	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
32	chr2:55463600-55470600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:55463600-55472400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:55463600-55474800	Weak transcription	Thymus	Thymus
35	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:55463800-55471600	Weak transcription	Psoas Muscle	Psoas
37	chr2:55463800-55475400	Weak transcription	Esophagus	oesophagus
38	chr2:55463800-55479600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55464000-55470600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:55464000-55476200	Weak transcription	Fetal Kidney	kidney
45	chr2:55464200-55473600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:55464400-55472400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:55464400-55472400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:55464400-55476200	Weak transcription	Brain Angular Gyrus	brain
49	chr2:55464400-55479600	Weak transcription	NHLF	lung
50	chr2:55464600-55475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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