Variant report

Variant	rs1857907
Chromosome Location	chr11:18554337-18554338
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18551902..18554921-chr11:18560952..18564096,3	K562	blood:
2	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:
3	chr11:18553476..18555204-chr11:18655804..18658130,2	MCF-7	breast:
4	chr11:18552647..18555345-chr20:55842668..55844786,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction
ENSG00000179119	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10500836	0.86[JPT][hapmap]
rs10741745	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10741746	0.96[ASN][1000 genomes]
rs10741747	0.85[JPT][hapmap]
rs10766485	0.86[JPT][hapmap]
rs10832940	0.92[JPT][hapmap]
rs10832941	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024694	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024711	0.93[JPT][hapmap]
rs11024717	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12224694	0.93[JPT][hapmap]
rs12361289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12419063	0.86[JPT][hapmap]
rs12577346	0.86[JPT][hapmap]
rs1395319	0.92[JPT][hapmap]
rs1395320	0.93[JPT][hapmap]
rs2132302	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291752	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2643866	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2658552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2658554	0.88[ASN][1000 genomes]
rs2658564	0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2658567	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698567	0.87[ASN][1000 genomes]
rs3925781	0.86[JPT][hapmap]
rs4298881	0.86[JPT][hapmap]
rs4756949	0.93[JPT][hapmap]
rs4756950	0.86[JPT][hapmap]
rs6486430	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6486434	0.93[JPT][hapmap]
rs7105889	0.93[JPT][hapmap]
rs7107057	0.93[JPT][hapmap]
rs7119085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7129164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7928872	0.93[JPT][hapmap]
rs7931630	0.93[JPT][hapmap]
rs7940645	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers 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	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1857907	TSG101	cis	multi-tissue	Pritchard
rs1857907	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549000-18576400	Weak transcription	Gastric	stomach
2	chr11:18549000-18577000	Weak transcription	Spleen	Spleen
3	chr11:18549200-18568200	Weak transcription	Lung	lung
4	chr11:18549200-18577000	Weak transcription	Esophagus	oesophagus
5	chr11:18549200-18583400	Weak transcription	Small Intestine	intestine
6	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:18549400-18555200	Weak transcription	Aorta	Aorta
8	chr11:18549400-18576000	Weak transcription	Ovary	ovary
9	chr11:18549400-18576400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:18549400-18577000	Weak transcription	Colonic Mucosa	Colon
11	chr11:18549400-18579200	Weak transcription	Pancreas	Pancrea
12	chr11:18549400-18583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:18549600-18555200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:18549600-18555200	Weak transcription	Adipose Nuclei	Adipose
16	chr11:18549600-18555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:18549600-18555400	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:18549600-18555400	Weak transcription	HSMMtube	muscle
19	chr11:18549600-18557800	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:18549600-18565000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:18549600-18565400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:18549600-18565800	Weak transcription	Brain Germinal Matrix	brain
23	chr11:18549600-18567600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:18549600-18568000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:18549600-18568400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:18549600-18575000	Weak transcription	Fetal Brain Female	brain
27	chr11:18549600-18575200	Weak transcription	Fetal Kidney	kidney
28	chr11:18549600-18576400	Weak transcription	Brain Substantia Nigra	brain
29	chr11:18549600-18576600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:18549600-18576800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:18549600-18577200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:18549600-18577800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
34	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
36	chr11:18549800-18554800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:18549800-18555000	Weak transcription	Fetal Intestine Large	intestine
38	chr11:18549800-18555200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:18549800-18555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:18549800-18555200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:18549800-18555200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:18549800-18555200	Weak transcription	Fetal Stomach	stomach
43	chr11:18549800-18555200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:18549800-18557200	Weak transcription	Psoas Muscle	Psoas
45	chr11:18549800-18557800	Weak transcription	NH-A	brain
46	chr11:18549800-18561200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:18549800-18564800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:18549800-18565000	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:18549800-18565400	Weak transcription	Fetal Lung	lung
50	chr11:18549800-18565600	Weak transcription	HMEC	breast

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