Variant report

Variant	rs3816248
Chromosome Location	chr4:77101068-77101069
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:77100858..77102558-chr4:77153141..77154759,2	MCF-7	breast:
2	chr4:77058522..77060950-chr4:77099295..77101938,2	MCF-7	breast:
3	chr4:77100761..77101387-chr4:77166867..77167817,2	MCF-7	breast:
4	chr4:77100837..77101592-chr4:77342165..77343074,2	MCF-7	breast:
5	chr4:77100730..77101561-chr4:77288471..77289108,2	K562	blood:
6	chr4:77100834..77101731-chr4:77299299..77299831,3	MCF-7	breast:
7	chr4:77100949..77101635-chr4:77228106..77229106,2	MCF-7	breast:
8	chr4:77099739..77102113-chr4:77107352..77109592,2	K562	blood:
9	chr4:77101037..77101657-chr4:77425834..77426647,3	K562	blood:
10	chr4:77100696..77102107-chr4:77298493..77299821,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163749	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10008834	1.00[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10015467	0.86[GIH][hapmap]
rs10028141	0.88[CHB][hapmap]
rs11097262	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11944608	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11946079	0.83[JPT][hapmap]
rs11947458	0.83[JPT][hapmap]
rs13141895	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1372409	0.81[ASN][1000 genomes]
rs17001573	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465660	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28563976	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4339237	0.84[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs6532189	0.86[GIH][hapmap]
rs6824953	0.88[ASN][1000 genomes]
rs6825004	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs9307076	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv995458	chr4:77093764-77102178	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3816248	NAAA	cis	lymphoblastoid	seeQTL
rs3816248	CXCL9	cis	lymphoblastoid	seeQTL
rs3816248	FGF5	cis	parietal	SCAN
rs3816248	NAAA	cis	parietal	SCAN
rs3816248	CXCL10	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:77071200-77113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77079400-77101400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr4:77079400-77108200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr4:77079600-77101200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:77079600-77101400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
8	chr4:77080800-77101200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:77080800-77101200	Strong transcription	NHDF-Ad	bronchial
10	chr4:77082400-77101400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:77083200-77112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:77087000-77101400	Strong transcription	Fetal Lung	lung
13	chr4:77088200-77101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:77090000-77113600	Weak transcription	A549	lung
15	chr4:77090200-77113000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
17	chr4:77090400-77107000	Weak transcription	Aorta	Aorta
18	chr4:77091000-77114200	Weak transcription	HMEC	breast
19	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
20	chr4:77095000-77113400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:77095400-77101200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:77095400-77107000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:77095600-77103600	Weak transcription	NHEK	skin
24	chr4:77095800-77107000	Weak transcription	Esophagus	oesophagus
25	chr4:77096200-77107000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:77096200-77107000	Weak transcription	Spleen	Spleen
27	chr4:77096200-77113200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:77096200-77113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:77096600-77107000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:77096600-77107000	Weak transcription	Gastric	stomach
31	chr4:77096800-77114000	Weak transcription	Small Intestine	intestine
32	chr4:77097000-77113200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:77097000-77113200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:77097000-77113200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr4:77097200-77102400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:77097200-77112400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:77097200-77113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:77097400-77113400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:77097400-77113400	Weak transcription	Fetal Brain Male	brain
40	chr4:77097400-77115000	Weak transcription	NH-A	brain
41	chr4:77097600-77106600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:77097600-77107000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:77097600-77119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:77097800-77113400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:77098000-77101200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:77098000-77101200	Weak transcription	Lung	lung
47	chr4:77098000-77113000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:77098600-77101400	Strong transcription	Dnd41	blood
49	chr4:77098600-77101600	Enhancers	Brain Hippocampus Middle	brain
50	chr4:77098800-77101200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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