Variant report

Variant	rs1376947
Chromosome Location	chr11:85990266-85990267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85988589..85992349-chr11:86011811..86014715,3	MCF-7	breast:
2	chr11:85988810..85991753-chr11:85992813..85995061,2	MCF-7	breast:
3	chr11:85989760..85992310-chr11:86001977..86004661,2	MCF-7	breast:
4	chr11:85986570..85988252-chr11:85990111..85992290,2	MCF-7	breast:
5	chr11:85990243..85992364-chr11:85993264..85996035,2	K562	blood:
6	chr11:85986924..85991339-chr11:85991702..85995217,5	K562	blood:
7	chr11:85990195..85992374-chr11:86002425..86005252,2	K562	blood:

Variant related genes	Relation type
ENSG00000254783	Chromatin interaction
ENSG00000149196	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10751138	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10792840	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10792847	0.81[TSI][hapmap]
rs10898450	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898454	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898455	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898456	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234582	0.87[CHD][hapmap]
rs11234583	0.92[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11234585	0.87[ASN][1000 genomes]
rs11234586	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234587	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11234591	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234592	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234595	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1215001	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225782	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12226796	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12282663	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574118	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577739	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12800606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1391221	0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs19039	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2173281	0.82[CHD][hapmap]
rs2600950	0.80[AMR][1000 genomes]
rs2600951	0.81[TSI][hapmap]
rs2646727	0.81[TSI][hapmap]
rs2646732	0.81[ASN][1000 genomes]
rs2847470	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2847471	0.81[TSI][hapmap]
rs291203	0.81[ASN][1000 genomes]
rs291215	0.89[CEU][hapmap];0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs291216	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs291220	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs291221	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs291225	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs291227	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291228	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291230	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291231	0.91[CEU][hapmap];0.81[CHD][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs291232	0.95[EUR][1000 genomes]
rs291233	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291234	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs291235	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs291236	0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs291237	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291238	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291242	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs291247	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs291251	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291252	0.80[TSI][hapmap]
rs34095340	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34972740	0.87[ASN][1000 genomes]
rs3923738	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4547120	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944562	0.90[EUR][1000 genomes]
rs7106569	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7937597	0.82[AFR][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	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	nsv898055	chr11:85968623-86000757	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv508643	chr11:85988577-86047719	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1376947	LRRC58	trans	parietal	SCAN
rs1376947	EED	Cis_1M	lymphoblastoid	RTeQTL
rs1376947	EED	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957200-85995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
3	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
4	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:85958400-85997200	Weak transcription	Brain Germinal Matrix	brain
6	chr11:85959200-85997600	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:85959400-85995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:85961000-85996000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:85961000-85997000	Weak transcription	Stomach Mucosa	stomach
10	chr11:85961600-85998000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:85964000-85995000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:85966000-85992000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:85966200-85991600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:85967000-85991600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:85969200-85995200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:85973000-85995000	Weak transcription	Lung	lung
17	chr11:85973000-85995000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:85973000-85995600	Weak transcription	Small Intestine	intestine
19	chr11:85973400-85995000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:85973800-85992800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:85973800-85995000	Weak transcription	Fetal Brain Female	brain
22	chr11:85974200-85995200	Weak transcription	Esophagus	oesophagus
23	chr11:85974800-85995000	Weak transcription	Right Ventricle	heart
24	chr11:85974800-85995000	Weak transcription	Thymus	Thymus
25	chr11:85974800-85995200	Weak transcription	Aorta	Aorta
26	chr11:85974800-86000000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:85975000-86002600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:85975400-85995000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:85975400-85995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:85976600-85995200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:85979000-85992400	Strong transcription	Dnd41	blood
32	chr11:85979600-85991600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:85980200-85991400	Strong transcription	Primary T cells from cord blood	blood
34	chr11:85981200-85992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:85983200-85991600	Strong transcription	Fetal Intestine Large	intestine
36	chr11:85983600-85992200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:85983800-85992000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:85984000-85991200	Strong transcription	Fetal Thymus	thymus
39	chr11:85984000-85991600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:85984000-85992200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:85984000-85992200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr11:85984400-85995000	Weak transcription	Fetal Stomach	stomach
43	chr11:85984400-86002800	Weak transcription	Fetal Intestine Small	intestine
44	chr11:85984600-85991200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:85985200-85991400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:85985800-85995000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:85986000-85990400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:85986000-85991600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:85986000-85992200	Strong transcription	Primary B cells from cord blood	blood
50	chr11:85986000-85995000	Weak transcription	Gastric	stomach

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