Variant report

Variant	rs11739280
Chromosome Location	chr5:96074147-96074148
allele	A/G
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	PAX5	chr5:96074021-96074244	GM12878	blood:	n/a	chr5:96074195-96074212

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96069238..96072291-chr5:96073506..96076761,3	MCF-7	breast:
2	chr5:96068554..96071240-chr5:96073251..96075210,2	K562	blood:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10447215	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10515244	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515246	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs11738135	0.85[EUR][1000 genomes]
rs11744642	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11745122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750399	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750400	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750510	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12186366	0.86[EUR][1000 genomes]
rs12188168	0.86[EUR][1000 genomes]
rs1559085	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17082200	0.85[EUR][1000 genomes]
rs17086588	0.85[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs17400685	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17400741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17401901	0.86[EUR][1000 genomes]
rs17402639	0.87[EUR][1000 genomes]
rs17405676	0.89[MEX][hapmap]
rs17478897	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17479052	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34942552	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55695458	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56116814	0.84[EUR][1000 genomes]
rs56122780	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56257788	0.85[EUR][1000 genomes]
rs6864233	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72772090	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72772091	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72772092	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72772095	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72773906	0.86[EUR][1000 genomes]
rs72773912	0.87[EUR][1000 genomes]
rs72773919	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11739280	CAST	cis	parietal	SCAN
rs11739280	CAST	cis	cerebellum	SCAN
rs11739280	CAST	cis	multi-tissue	Pritchard
rs11739280	C5orf36	cis	cerebellum	SCAN
rs11739280	ERAP1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
2	chr5:96051200-96076800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:96054800-96077200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:96057800-96075200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:96057800-96076000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:96057800-96098600	Weak transcription	Fetal Brain Male	brain
7	chr5:96058000-96077200	Weak transcription	Small Intestine	intestine
8	chr5:96058000-96078200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:96062800-96081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:96064600-96092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96066400-96074400	Weak transcription	Colonic Mucosa	Colon
13	chr5:96066600-96076000	Weak transcription	Aorta	Aorta
14	chr5:96066600-96076000	Weak transcription	Gastric	stomach
15	chr5:96066600-96076000	Weak transcription	Spleen	Spleen
16	chr5:96066600-96076800	Weak transcription	Fetal Thymus	thymus
17	chr5:96066800-96077200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:96066800-96079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:96067200-96074200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:96067200-96076600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:96068200-96077200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr5:96068200-96095400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:96068200-96100400	Strong transcription	Liver	Liver
24	chr5:96068400-96077400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:96069200-96077200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr5:96069400-96094000	Strong transcription	Fetal Muscle Leg	muscle
29	chr5:96069600-96094000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:96069800-96077400	Strong transcription	Primary B cells from cord blood	blood
31	chr5:96070200-96075000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:96070200-96077400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:96070200-96083400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:96070200-96087800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:96070200-96116400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:96070400-96076800	Strong transcription	Fetal Intestine Large	intestine
37	chr5:96070400-96077200	Weak transcription	Stomach Mucosa	stomach
38	chr5:96070600-96079200	Strong transcription	Placenta	Placenta
39	chr5:96070800-96095400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:96071000-96078400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:96071000-96112800	Strong transcription	Hela-S3	cervix
42	chr5:96071200-96077200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:96071200-96078600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:96071200-96085000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:96071200-96088000	Strong transcription	A549	lung
46	chr5:96071200-96094000	Strong transcription	HSMM	muscle
47	chr5:96071400-96078400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:96071400-96078600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:96071400-96078600	Weak transcription	Right Atrium	heart
50	chr5:96071400-96113000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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