Variant report

Variant	rs10896139
Chromosome Location	chr11:66650060-66650061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66620817..66623976-chr11:66646170..66651314,5	MCF-7	breast:
2	chr11:66640579..66644175-chr11:66648917..66652443,5	MCF-7	breast:
3	chr11:66382706..66385676-chr11:66647660..66650691,4	MCF-7	breast:
4	chr11:66649204..66651598-chr11:66653844..66656638,2	MCF-7	breast:
5	chr11:66632881..66640228-chr11:66642679..66650860,16	MCF-7	breast:
6	chr11:66647175..66649166-chr11:66649230..66650803,2	MCF-7	breast:
7	chr11:66511692..66514544-chr11:66648190..66650243,2	MCF-7	breast:
8	chr11:66648193..66651672-chr17:57913851..57917010,3	MCF-7	breast:
9	chr11:66608285..66612923-chr11:66645683..66650712,11	MCF-7	breast:
10	chr11:66622039..66625017-chr11:66649719..66652504,2	K562	blood:
11	chr11:66607636..66611821-chr11:66647654..66651016,8	MCF-7	breast:
12	chr11:66622201..66627158-chr11:66645726..66651981,9	MCF-7	breast:
13	chr11:66647060..66650897-chr11:66788816..66791425,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction
ENSG00000173227	Chromatin interaction
ENSG00000173653	Chromatin interaction
ENSG00000173715	Chromatin interaction
ENSG00000173621	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000248643	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10750790	0.95[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10791889	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs10791892	0.83[EUR][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11227610	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs11600959	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2077432	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2167457	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2187041	0.90[CEU][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2380760	0.91[EUR][1000 genomes]
rs3741194	0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3741364	0.82[GIH][hapmap]
rs4008953	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4576826	0.83[EUR][1000 genomes]
rs4930184	0.81[EUR][1000 genomes]
rs4930390	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6591222	0.91[CEU][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs7103627	0.90[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7119426	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7120256	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7122539	0.86[TSI][hapmap]
rs714766	0.83[EUR][1000 genomes]
rs7570	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7930203	0.95[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7948839	0.95[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9971487	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10896139	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs10896139	EHBP1L1	cis	cerebellum	SCAN
rs10896139	C11orf80	cis	cerebellum	SCAN
rs10896139	CTSF	cis	multi-tissue	Pritchard
rs10896139	LRFN4	cis	multi-tissue	Pritchard
rs10896139	RARRES3	cis	parietal	SCAN
rs10896139	B3GNT1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:66625800-66650800	Weak transcription	Osteobl	bone
3	chr11:66636800-66650800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:66638600-66650200	Weak transcription	Fetal Intestine Large	intestine
5	chr11:66639000-66657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:66639200-66657400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:66639400-66650400	Weak transcription	Aorta	Aorta
8	chr11:66639400-66659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:66639600-66650200	Weak transcription	Fetal Intestine Small	intestine
10	chr11:66643200-66651400	Enhancers	Fetal Muscle Leg	muscle
11	chr11:66643200-66653000	Enhancers	Liver	Liver
12	chr11:66644600-66650800	Weak transcription	HepG2	liver
13	chr11:66645200-66652000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:66645400-66651200	Enhancers	Gastric	stomach
15	chr11:66645400-66651200	Enhancers	HMEC	breast
16	chr11:66645600-66650800	Enhancers	Fetal Thymus	thymus
17	chr11:66645600-66652400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:66645800-66651400	Enhancers	HSMMtube	muscle
19	chr11:66646000-66660800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:66646200-66650200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:66646200-66651400	Enhancers	Fetal Brain Male	brain
22	chr11:66646400-66650200	Enhancers	Brain Cingulate Gyrus	brain
23	chr11:66646400-66650200	Genic enhancers	NHEK	skin
24	chr11:66646600-66650800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:66646600-66651400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:66646800-66650200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr11:66646800-66650400	Weak transcription	NHLF	lung
28	chr11:66646800-66650800	Weak transcription	NHDF-Ad	bronchial
29	chr11:66646800-66651400	Enhancers	Adipose Nuclei	Adipose
30	chr11:66647000-66650800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:66647000-66651200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr11:66647400-66650400	Enhancers	Brain Angular Gyrus	brain
33	chr11:66647400-66650800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:66647600-66650200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr11:66647600-66650200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr11:66647600-66651000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:66647600-66653400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr11:66647800-66651000	Enhancers	Fetal Lung	lung
39	chr11:66647800-66651200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr11:66648000-66650200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:66648000-66650400	Enhancers	Esophagus	oesophagus
42	chr11:66648000-66650400	Enhancers	Pancreas	Pancrea
43	chr11:66648000-66650800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:66648200-66651200	Enhancers	Fetal Heart	heart
45	chr11:66648400-66651000	Weak transcription	HUVEC	blood vessel
46	chr11:66648600-66650200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:66648600-66650200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:66648600-66650200	Enhancers	A549	lung
49	chr11:66648600-66651400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:66648600-66652400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links