Variant report

Variant	rs1540180
Chromosome Location	chr11:77259574-77259575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76901170..76903314-chr11:77259087..77261522,2	MCF-7	breast:
2	chr11:76906559..76907619-chr11:77259021..77259968,8	MCF-7	breast:
3	chr11:76906576..76907452-chr11:77259126..77259917,4	MCF-7	breast:
4	chr11:77259201..77259776-chr11:77330654..77331222,2	MCF-7	breast:
5	chr11:76902791..76903778-chr11:77258737..77260363,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074201	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11237217	0.92[ASN][1000 genomes]
rs1540181	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1970749	0.82[EUR][1000 genomes]
rs2013296	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4572159	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4945179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945181	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945188	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58219609	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592726	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592735	0.92[ASN][1000 genomes]
rs7115612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7946637	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9634032	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1540180	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77258400-77260000	Enhancers	H1 Cell Line	embryonic stem cell
2	chr11:77258400-77260000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr11:77258600-77260000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr11:77258600-77260600	Enhancers	Fetal Intestine Small	intestine
5	chr11:77258800-77259800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:77258800-77260000	Enhancers	Stomach Mucosa	stomach
7	chr11:77259000-77259600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:77259000-77259800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:77259000-77259800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:77259000-77259800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr11:77259000-77259800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:77259000-77259800	Enhancers	Brain Cingulate Gyrus	brain
13	chr11:77259000-77259800	Enhancers	Brain Substantia Nigra	brain
14	chr11:77259000-77259800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr11:77259000-77259800	Enhancers	GM12878-XiMat	blood
16	chr11:77259000-77260000	Enhancers	Brain Hippocampus Middle	brain
17	chr11:77259000-77260000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr11:77259000-77260000	Enhancers	Duodenum Mucosa	Duodenum
19	chr11:77259000-77260000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr11:77259000-77260200	Enhancers	Fetal Intestine Large	intestine
21	chr11:77259000-77260400	Enhancers	Brain Angular Gyrus	brain
22	chr11:77259000-77260800	Enhancers	Placenta	Placenta
23	chr11:77259000-77270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:77259200-77259600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr11:77259200-77259600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr11:77259200-77259800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr11:77259200-77259800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr11:77259200-77259800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:77259200-77259800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr11:77259200-77259800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:77259200-77259800	Enhancers	Liver	Liver
32	chr11:77259200-77259800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:77259200-77259800	Enhancers	Colon Smooth Muscle	Colon
34	chr11:77259200-77259800	Enhancers	HSMMtube	muscle
35	chr11:77259200-77259800	Enhancers	NH-A	brain
36	chr11:77259200-77259800	Enhancers	Osteobl	bone
37	chr11:77259200-77260000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:77259200-77260000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr11:77259200-77260200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:77259400-77259600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr11:77259400-77259800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr11:77259400-77259800	Enhancers	Brain Anterior Caudate	brain
43	chr11:77259400-77259800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr11:77259400-77261200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links