Variant report

Variant	rs11727086
Chromosome Location	chr4:99828368-99828369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99822851..99824917-chr4:99827424..99830056,2	K562	blood:
2	chr4:99827732..99830056-chr4:99838507..99841404,2	K562	blood:
3	chr4:99821499..99832064-chr4:99845860..99851281,12	MCF-7	breast:
4	chr4:99825609..99828842-chr4:99829565..99832831,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249055	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000263923	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1154412	1.00[ASN][1000 genomes]
rs11722494	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727079	0.95[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731092	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735758	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736580	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107184	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107892	0.87[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110878	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115072	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115688	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124855	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127259	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130454	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133934	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13832	1.00[ASN][1000 genomes]
rs17511498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17583053	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004994	1.00[ASN][1000 genomes]
rs2165944	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2230574	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018048	1.00[ASN][1000 genomes]
rs34073334	0.89[AFR][1000 genomes]
rs34116542	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164768	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34445885	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34552530	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34849916	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019647	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35360485	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35619083	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885444	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36061550	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699369	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699689	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699692	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323189	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323190	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323206	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67650226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692635	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7688221	0.87[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688461	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896992	1.00[ASN][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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11727086	ROBO1	trans	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99801600-99829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:99802800-99830200	Weak transcription	Ovary	ovary
3	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
4	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:99804600-99838400	Weak transcription	Esophagus	oesophagus
6	chr4:99805200-99832000	Weak transcription	Spleen	Spleen
7	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
8	chr4:99807800-99832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:99808000-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:99808600-99830600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99815800-99848200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:99816600-99831200	Weak transcription	Brain Anterior Caudate	brain
14	chr4:99816600-99847200	Weak transcription	Fetal Brain Male	brain
15	chr4:99817000-99830800	Weak transcription	Brain Germinal Matrix	brain
16	chr4:99819000-99831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:99819200-99829400	Weak transcription	Fetal Brain Female	brain
18	chr4:99822200-99829800	Weak transcription	A549	lung
19	chr4:99822800-99829400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:99822800-99830000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:99822800-99830600	Weak transcription	Left Ventricle	heart
22	chr4:99822800-99831800	Weak transcription	Fetal Stomach	stomach
23	chr4:99823000-99828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:99823000-99828800	Weak transcription	HUVEC	blood vessel
25	chr4:99823000-99829400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:99823000-99829400	Weak transcription	Fetal Kidney	kidney
27	chr4:99823000-99829400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:99823000-99830000	Weak transcription	Liver	Liver
29	chr4:99823000-99835600	Weak transcription	Adipose Nuclei	Adipose
30	chr4:99823000-99836000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:99823000-99841600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:99823000-99842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:99823000-99845600	Weak transcription	Hela-S3	cervix
34	chr4:99823000-99847200	Weak transcription	Thymus	Thymus
35	chr4:99823000-99848800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:99823000-99849000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:99823000-99849200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:99823200-99828800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:99823200-99829200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:99823200-99830000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:99823200-99830200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:99823200-99830600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:99823200-99830800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:99823200-99831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:99823200-99831600	Weak transcription	Fetal Lung	lung
46	chr4:99823200-99839600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:99823200-99847800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:99823200-99848000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:99823200-99848600	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:99823200-99848800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links