Variant report

Variant	rs11748362
Chromosome Location	chr5:126142260-126142261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126111922..126114546-chr5:126139894..126142503,2	K562	blood:
2	chr5:126111122..126113687-chr5:126141922..126143710,2	MCF-7	breast:
3	chr5:126111922..126113626-chr5:126139894..126142741,2	K562	blood:
4	chr5:126140909..126142452-chr5:126150010..126152281,2	K562	blood:

Variant related genes	Relation type
ENSG00000113368	Chromatin interaction
ENSG00000251072	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11241908	0.90[EUR][1000 genomes]
rs11241910	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741648	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11748369	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12514715	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12523041	0.83[CHD][hapmap]
rs12655469	0.82[JPT][hapmap]
rs13176550	0.90[EUR][1000 genomes]
rs13181450	0.90[EUR][1000 genomes]
rs17598783	0.83[CHD][hapmap]
rs1964723	0.92[EUR][1000 genomes]
rs2036847	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2271352	0.84[JPT][hapmap]
rs2408776	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34740558	0.91[ASN][1000 genomes]
rs35091677	0.90[EUR][1000 genomes]
rs35156477	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35500127	0.91[EUR][1000 genomes]
rs3805738	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3805744	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828699	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57812062	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6595736	0.88[EUR][1000 genomes]
rs6595738	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6873056	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6873780	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6874037	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6894559	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7708419	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7709312	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11748362	GLI4	trans	brain	seeQTL
rs11748362	FBN2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126114600-126161600	Weak transcription	Ovary	ovary
2	chr5:126115800-126145800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:126116400-126143400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:126116600-126147800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:126125400-126146600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:126128800-126145800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:126130400-126165800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:126132200-126161200	Weak transcription	Gastric	stomach
9	chr5:126135200-126147200	Weak transcription	Fetal Brain Male	brain
10	chr5:126136000-126145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:126136000-126175200	Strong transcription	Dnd41	blood
12	chr5:126136400-126162400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:126137600-126146800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:126137600-126154600	Weak transcription	Fetal Kidney	kidney
15	chr5:126137600-126166600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:126137800-126146400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:126137800-126147400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:126138400-126146000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:126139800-126144200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:126139800-126148200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:126139800-126160600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:126139800-126175400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:126140000-126142400	Strong transcription	K562	blood
24	chr5:126140000-126146600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:126140000-126150600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:126140000-126162000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:126140000-126162200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:126140000-126175200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:126140000-126175400	Strong transcription	Fetal Thymus	thymus
30	chr5:126140200-126143000	Strong transcription	A549	lung
31	chr5:126140200-126143400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:126140200-126150600	Strong transcription	Thymus	Thymus
33	chr5:126140200-126161400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:126140200-126161800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:126140200-126162600	Weak transcription	Colonic Mucosa	Colon
36	chr5:126140200-126163400	Weak transcription	Pancreas	Pancrea
37	chr5:126140400-126142400	Strong transcription	Fetal Lung	lung
38	chr5:126140400-126142600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr5:126140400-126142800	Strong transcription	Fetal Intestine Large	intestine
40	chr5:126140400-126143000	Strong transcription	HepG2	liver
41	chr5:126140400-126147200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:126140400-126150000	Strong transcription	Fetal Muscle Leg	muscle
43	chr5:126140400-126150600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr5:126140400-126161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:126140400-126161800	Weak transcription	Placenta	Placenta
46	chr5:126140400-126162200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:126140600-126143400	Strong transcription	GM12878-XiMat	blood
48	chr5:126140600-126161600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:126140800-126142600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:126140800-126142800	Strong transcription	Fetal Brain Female	brain

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