Variant report

Variant	rs28104
Chromosome Location	chr5:96039031-96039032
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70820351..70820933-chr5:96038574..96039212,2	Hela-S3	cervix:
2	chr17:43225533..43226190-chr5:96038965..96039627,2	Hela-S3	cervix:
3	chr5:96038474..96039975-chr5:96271296..96273305,2	MCF-7	breast:
4	chr5:95997693..95999480-chr5:96036950..96039552,2	MCF-7	breast:
5	chr5:96038598..96039099-chr8:48873175..48874058,2	Hela-S3	cervix:
6	chr2:211035016..211035669-chr5:96038518..96039212,2	Hela-S3	cervix:
7	chr5:95998068..96000217-chr5:96038673..96040696,2	MCF-7	breast:
8	chr5:96038597..96040371-chr5:96076002..96079687,4	K562	blood:
9	chr5:96035534..96040371-chr5:96075768..96079687,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction
ENSG00000249180	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000144445	Chromatin interaction
ENSG00000104738	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10067766	0.85[JPT][hapmap]
rs1421911	0.86[JPT][hapmap]
rs151835	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs151904	0.86[JPT][hapmap]
rs152005	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs152014	0.86[JPT][hapmap]
rs152017	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs152020	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs17086598	0.89[AFR][1000 genomes]
rs2351245	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs26482	0.86[JPT][hapmap]
rs26483	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs26484	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs26485	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs26503	0.86[JPT][hapmap]
rs26504	0.86[JPT][hapmap]
rs28093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs31248	0.86[JPT][hapmap]
rs31249	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs31250	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4590196	0.86[JPT][hapmap]
rs6556937	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6860934	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6897588	0.86[JPT][hapmap]
rs7704167	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7705824	0.86[JPT][hapmap]
rs7733671	0.86[JPT][hapmap]

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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28104	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96037600-96039200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr5:96037800-96039200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:96037800-96039200	Active TSS	Hela-S3	cervix
4	chr5:96038000-96039200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:96038000-96039200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:96038000-96039200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:96038000-96039200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:96038000-96039200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:96038000-96039200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr5:96038000-96039200	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr5:96038000-96039200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr5:96038000-96039200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:96038000-96039200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:96038000-96039200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:96038000-96039200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:96038000-96039200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:96038000-96039200	Active TSS	Colon Smooth Muscle	Colon
18	chr5:96038000-96039200	Active TSS	Fetal Kidney	kidney
19	chr5:96038000-96039200	Active TSS	Fetal Stomach	stomach
20	chr5:96038000-96039200	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr5:96038000-96039200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr5:96038000-96039400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:96038000-96039400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr5:96038000-96039400	Active TSS	Liver	Liver
25	chr5:96038000-96039400	Active TSS	Brain Anterior Caudate	brain
26	chr5:96038000-96039400	Active TSS	Brain Cingulate Gyrus	brain
27	chr5:96038000-96039400	Active TSS	Brain Germinal Matrix	brain
28	chr5:96038000-96039400	Active TSS	Brain Hippocampus Middle	brain
29	chr5:96038000-96039400	Active TSS	Brain Substantia Nigra	brain
30	chr5:96038000-96039400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr5:96038000-96039400	Active TSS	Fetal Intestine Large	intestine
32	chr5:96038000-96039400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr5:96038000-96039400	Active TSS	NHDF-Ad	bronchial
34	chr5:96038000-96039600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr5:96038000-96039600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:96038000-96039600	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:96038000-96039600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:96038000-96039600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:96038000-96039600	Active TSS	Duodenum Mucosa	Duodenum
40	chr5:96038000-96039600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:96038000-96039600	Active TSS	Ovary	ovary
42	chr5:96038000-96039800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr5:96038000-96040000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr5:96038000-96040000	Active TSS	Right Atrium	heart
45	chr5:96038000-96040200	Active TSS	Brain Angular Gyrus	brain
46	chr5:96038000-96040800	Active TSS	Psoas Muscle	Psoas
47	chr5:96038200-96039200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:96038200-96039200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:96038200-96039200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr5:96038200-96039200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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