Variant report

Variant	rs28759823
Chromosome Location	chr4:76844849-76844850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:76844801-76844909	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76844405..76846059-chr4:76849294..76850963,2	MCF-7	breast:

Variant related genes	Relation type
NAAA	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518142	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11490704	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1876096	0.86[ASN][1000 genomes]
rs2047987	0.86[ASN][1000 genomes]
rs2047988	0.84[ASN][1000 genomes]
rs2135232	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280101	0.86[ASN][1000 genomes]
rs3733233	0.82[EUR][1000 genomes]
rs3733234	0.82[EUR][1000 genomes]
rs3733235	0.82[EUR][1000 genomes]
rs55967764	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317633	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823734	0.86[ASN][1000 genomes]
rs72651374	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686066	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905958	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28759823	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs28759823	ASAHL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76832600-76859000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:76833800-76851200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:76833800-76856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
5	chr4:76834000-76847000	Strong transcription	Primary T cells from cord blood	blood
6	chr4:76834200-76851200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:76835000-76847200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr4:76835000-76847400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:76835000-76859400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:76835000-76859600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:76835200-76859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:76835400-76845200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:76835400-76845400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:76836800-76847400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:76837000-76851400	Weak transcription	Fetal Thymus	thymus
16	chr4:76837000-76857200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:76837000-76860200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:76837200-76845000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:76837200-76860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:76837200-76860800	Weak transcription	HSMM	muscle
21	chr4:76837600-76845200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:76837600-76845600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:76837600-76851400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:76837600-76858400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:76837600-76859200	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:76837600-76860800	Weak transcription	Fetal Kidney	kidney
27	chr4:76837800-76860800	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:76837800-76860800	Weak transcription	NH-A	brain
29	chr4:76838000-76845200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:76838000-76847000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:76838000-76857600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:76838200-76846800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:76838200-76847200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:76838200-76852600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:76838400-76845800	Strong transcription	Adipose Nuclei	Adipose
36	chr4:76838600-76845400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:76838600-76851800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:76838600-76860800	Weak transcription	NHLF	lung
39	chr4:76839000-76860400	Weak transcription	HUVEC	blood vessel
40	chr4:76839400-76860800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:76839600-76847000	Strong transcription	Primary B cells from cord blood	blood
42	chr4:76839600-76847000	Strong transcription	Spleen	Spleen
43	chr4:76839600-76859200	Weak transcription	Brain Substantia Nigra	brain
44	chr4:76839800-76860800	Weak transcription	Psoas Muscle	Psoas
45	chr4:76839800-76860800	Weak transcription	HMEC	breast
46	chr4:76840000-76845600	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr4:76841000-76847200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:76841400-76845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:76841400-76845200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:76841400-76851400	Weak transcription	Hela-S3	cervix

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