Variant report

Variant	rs11750477
Chromosome Location	chr5:179922904-179922905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179920260..179922999-chr5:180038598..180040134,2	MCF-7	breast:
2	chr5:179920138..179923580-chr5:179954774..179958751,3	MCF-7	breast:
3	chr5:179778332..179781251-chr5:179920436..179923318,3	MCF-7	breast:
4	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction
ENSG00000113300	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000248367	Chromatin interaction
ENSG00000037280	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11249715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249724	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738060	0.83[EUR][1000 genomes]
rs11740103	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11740121	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11740213	0.90[EUR][1000 genomes]
rs11740953	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741030	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742350	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742375	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743486	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11744382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744428	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744582	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745477	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745688	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747624	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11748724	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748792	0.90[EUR][1000 genomes]
rs11750835	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11949203	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11950075	0.82[ASN][1000 genomes]
rs11956078	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960298	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12109328	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110046	0.86[EUR][1000 genomes]
rs12719870	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13154631	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13156947	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13164771	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13166694	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171609	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13171921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13174480	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179742	0.90[EUR][1000 genomes]
rs13182919	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13183429	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13187624	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17630549	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698422	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002074	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34281336	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34957777	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35076338	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35197594	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35490561	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35706747	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56005965	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56039468	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60034484	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62405495	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405496	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405525	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405531	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62405532	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62405547	0.89[EUR][1000 genomes]
rs71613462	0.80[AFR][1000 genomes]
rs872365	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs872366	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv3356496	chr5:179920371-179922919	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179920400-179923000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr5:179920400-179923200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:179920400-179923400	Active TSS	GM12878-XiMat	blood
4	chr5:179920600-179923000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:179920600-179923200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr5:179920800-179923000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:179920800-179923000	Active TSS	A549	lung
8	chr5:179920800-179923200	Active TSS	NHDF-Ad	bronchial
9	chr5:179921000-179923000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:179921000-179923000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179921000-179923200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:179921400-179923000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:179921400-179923000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:179922200-179923000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr5:179922200-179923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179922200-179923000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr5:179922200-179923000	Flanking Active TSS	Fetal Brain Female	brain
18	chr5:179922200-179923000	Flanking Active TSS	K562	blood
19	chr5:179922200-179923000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr5:179922200-179923200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:179922200-179923200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr5:179922200-179923200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr5:179922200-179923200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:179922200-179923200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:179922200-179923200	Flanking Active TSS	Fetal Lung	lung
26	chr5:179922200-179923200	Flanking Active TSS	HUVEC	blood vessel
27	chr5:179922200-179923400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr5:179922200-179923400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr5:179922200-179923400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:179922200-179923400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr5:179922200-179923600	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr5:179922200-179923800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:179922200-179923800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:179922400-179923000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr5:179922400-179923000	Flanking Active TSS	Fetal Brain Male	brain
36	chr5:179922400-179923000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:179922400-179923000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:179922400-179923000	Flanking Active TSS	NHEK	skin
39	chr5:179922400-179923200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:179922400-179923200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:179922400-179923200	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
42	chr5:179922400-179923400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
43	chr5:179922400-179923400	Enhancers	Small Intestine	intestine
44	chr5:179922400-179923400	Transcr. at gene 5' and 3'	Hela-S3	cervix
45	chr5:179922400-179923400	Flanking Active TSS	NH-A	brain
46	chr5:179922400-179923600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr5:179922400-179923600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr5:179922400-179923600	Enhancers	Spleen	Spleen
49	chr5:179922400-179923800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:179922400-179924000	Flanking Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links