Variant report

Variant	rs28615278
Chromosome Location	chr17:17903095-17903096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17901299..17904242-chr17:17926943..17929821,2	MCF-7	breast:
2	chr17:17901247..17903124-chr17:17907149..17909889,2	MCF-7	breast:
3	chr17:17903006..17906615-chr17:17908063..17910293,3	K562	blood:

Variant related genes	Relation type
ENSG00000171953	Chromatin interaction
ENSG00000171962	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12103467	1.00[CHD][hapmap]
rs12603505	1.00[CHD][hapmap]
rs16960878	1.00[EUR][1000 genomes]
rs16960959	1.00[CHD][hapmap]
rs16961971	1.00[EUR][1000 genomes]
rs16961993	1.00[EUR][1000 genomes]
rs16962003	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs17854924	1.00[CHD][hapmap]
rs28528721	1.00[EUR][1000 genomes]
rs28595155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924814	1.00[EUR][1000 genomes]
rs4924815	1.00[EUR][1000 genomes]
rs4924816	1.00[EUR][1000 genomes]
rs4924818	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs4924819	1.00[EUR][1000 genomes]
rs4925111	1.00[EUR][1000 genomes]
rs4925113	1.00[EUR][1000 genomes]
rs59019513	1.00[EUR][1000 genomes]
rs59531660	1.00[EUR][1000 genomes]
rs59754425	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502629	0.87[YRI][hapmap]
rs73295666	1.00[EUR][1000 genomes]
rs73979203	1.00[EUR][1000 genomes]
rs73979206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979207	1.00[EUR][1000 genomes]
rs73979241	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981070	1.00[EUR][1000 genomes]
rs73981075	1.00[EUR][1000 genomes]
rs73981078	1.00[EUR][1000 genomes]
rs7405940	1.00[EUR][1000 genomes]
rs8081943	1.00[EUR][1000 genomes]
rs9889565	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9895191	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9897573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9898044	1.00[EUR][1000 genomes]
rs9899537	1.00[EUR][1000 genomes]
rs9900884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9908994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9944449	1.00[EUR][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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3324863	chr17:17900927-17905625	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28615278	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17903200	Weak transcription	Gastric	stomach
2	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
3	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
4	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
6	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
8	chr17:17889000-17907400	Weak transcription	Brain Anterior Caudate	brain
9	chr17:17890000-17907400	Weak transcription	Brain Germinal Matrix	brain
10	chr17:17892200-17908400	Weak transcription	Lung	lung
11	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
13	chr17:17892800-17908000	Weak transcription	Spleen	Spleen
14	chr17:17894000-17903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
16	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:17895000-17903400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr17:17895200-17909600	Weak transcription	NHLF	lung
19	chr17:17898000-17909200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr17:17898000-17910800	Weak transcription	Brain Hippocampus Middle	brain
21	chr17:17898200-17908200	Weak transcription	Right Ventricle	heart
22	chr17:17898200-17908400	Weak transcription	Fetal Brain Female	brain
23	chr17:17898200-17909000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:17898400-17905600	Weak transcription	NHDF-Ad	bronchial
27	chr17:17898400-17907400	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:17898400-17910000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:17898400-17911400	Weak transcription	HSMM	muscle
30	chr17:17898600-17908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:17898600-17909800	Weak transcription	Adipose Nuclei	Adipose
32	chr17:17898600-17909800	Weak transcription	Ovary	ovary
33	chr17:17898600-17910600	Weak transcription	Placenta	Placenta
34	chr17:17898600-17910800	Weak transcription	Esophagus	oesophagus
35	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:17898800-17908800	Weak transcription	NHEK	skin
37	chr17:17899000-17904600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr17:17900200-17903400	Enhancers	Fetal Heart	heart
39	chr17:17900600-17903400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr17:17901200-17908200	Weak transcription	Fetal Stomach	stomach
41	chr17:17901200-17909200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:17901600-17907400	Weak transcription	Left Ventricle	heart
43	chr17:17902200-17907400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:17902400-17903200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr17:17902400-17903200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:17902400-17903400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:17902400-17903600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:17902600-17903600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:17902600-17904000	Enhancers	Fetal Intestine Large	intestine
50	chr17:17902600-17904000	Enhancers	HepG2	liver

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