Variant report

Variant	rs11079771
Chromosome Location	chr17:45372665-45372666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45369846..45373285-chr17:45374240..45379330,4	K562	blood:
2	chr17:45363175..45368028-chr17:45369299..45373237,4	K562	blood:
3	chr17:45371857..45373419-chr17:45389135..45391339,2	K562	blood:
4	chr17:45372166..45375464-chr17:45377689..45379653,5	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11867192	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11867253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11867589	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11868344	0.88[ASN][1000 genomes]
rs11869439	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11869487	1.00[CEU][hapmap]
rs11869768	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11869835	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11870252	0.88[ASN][1000 genomes]
rs11870334	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11870781	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11870948	1.00[CEU][hapmap]
rs11871031	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11871477	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12051664	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12051702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12051709	1.00[CEU][hapmap]
rs12051795	1.00[CEU][hapmap]
rs12162128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16941751	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16941771	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16941855	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16941861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1878067	0.88[CHB][hapmap]
rs2292700	0.87[CHB][hapmap]
rs2317676	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3785870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3785873	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs41304764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55706706	0.88[ASN][1000 genomes]
rs56722403	0.88[ASN][1000 genomes]
rs5919	0.87[CHB][hapmap]
rs73322309	0.86[ASN][1000 genomes]
rs8073229	0.87[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11079771	GGT5	trans	brain	seeQTL
rs11079771	MTNR1A	trans	brain	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45356800-45377200	Weak transcription	Fetal Intestine Large	intestine
2	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
3	chr17:45358200-45377200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr17:45360600-45373800	Strong transcription	Fetal Stomach	stomach
6	chr17:45368200-45372800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:45368600-45372800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:45369400-45373000	Enhancers	K562	blood
9	chr17:45369600-45373600	Strong transcription	Placenta	Placenta
10	chr17:45369800-45373400	Enhancers	Primary B cells from peripheral blood	blood
11	chr17:45370000-45376600	Weak transcription	Pancreas	Pancrea
12	chr17:45370000-45378000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:45371000-45377200	Weak transcription	Fetal Heart	heart
14	chr17:45371200-45372800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:45371200-45374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr17:45371200-45374000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr17:45371400-45372800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:45371400-45372800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:45371400-45372800	Enhancers	HSMMtube	muscle
20	chr17:45371400-45374400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr17:45371400-45374400	Enhancers	Brain Hippocampus Middle	brain
22	chr17:45371400-45393000	Weak transcription	Dnd41	blood
23	chr17:45371600-45372800	Genic enhancers	HUVEC	blood vessel
24	chr17:45371600-45373000	Enhancers	Right Ventricle	heart
25	chr17:45371600-45373400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:45371600-45373400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:45371600-45374000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:45371600-45374000	Enhancers	Brain Cingulate Gyrus	brain
29	chr17:45371600-45374000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:45371600-45374000	Enhancers	Brain Substantia Nigra	brain
31	chr17:45371600-45374200	Enhancers	Brain Angular Gyrus	brain
32	chr17:45371600-45374400	Enhancers	Brain Anterior Caudate	brain
33	chr17:45371800-45372800	Enhancers	Colonic Mucosa	Colon
34	chr17:45371800-45372800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr17:45371800-45373000	Enhancers	Aorta	Aorta
36	chr17:45371800-45373000	Genic enhancers	Colon Smooth Muscle	Colon
37	chr17:45371800-45373000	Enhancers	Ovary	ovary
38	chr17:45371800-45373200	Genic enhancers	Fetal Muscle Leg	muscle
39	chr17:45371800-45373600	Enhancers	Lung	lung
40	chr17:45371800-45373600	Enhancers	Right Atrium	heart
41	chr17:45371800-45373600	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr17:45371800-45373800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr17:45371800-45373800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr17:45371800-45374000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr17:45372000-45372800	Enhancers	Fetal Kidney	kidney
46	chr17:45372000-45372800	Enhancers	Fetal Lung	lung
47	chr17:45372000-45372800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
48	chr17:45372000-45373000	Enhancers	Left Ventricle	heart
49	chr17:45372000-45373600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:45372000-45373600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links