Variant report

Variant	rs11732850
Chromosome Location	chr4:76620803-76620804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76615229..76618143-chr4:76619781..76621972,2	K562	blood:
2	chr4:76620008..76622936-chr4:76627662..76629475,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10031352	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10856853	0.84[GIH][hapmap];0.92[JPT][hapmap]
rs11097121	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11556146	0.84[GIH][hapmap];0.92[JPT][hapmap]
rs11723767	0.84[JPT][hapmap]
rs11727895	0.80[ASN][1000 genomes]
rs11734358	0.81[ASN][1000 genomes]
rs11935073	0.92[JPT][hapmap]
rs12498415	0.82[GIH][hapmap];0.92[JPT][hapmap]
rs12508200	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508992	0.80[ASN][1000 genomes]
rs12511575	0.92[JPT][hapmap]
rs13137229	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16996019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17000786	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs17000794	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs17000864	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs186563	0.80[ASN][1000 genomes]
rs2089253	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs2175640	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28573275	0.80[ASN][1000 genomes]
rs28680723	0.80[ASN][1000 genomes]
rs324686	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs324688	0.80[ASN][1000 genomes]
rs324690	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs324691	0.80[ASN][1000 genomes]
rs324693	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324696	0.95[CEU][hapmap];0.80[ASN][1000 genomes]
rs324697	0.80[ASN][1000 genomes]
rs324698	0.80[ASN][1000 genomes]
rs324700	0.80[ASN][1000 genomes]
rs324701	0.80[ASN][1000 genomes]
rs324703	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324709	0.91[CEU][hapmap]
rs324712	0.80[ASN][1000 genomes]
rs324713	0.80[ASN][1000 genomes]
rs324714	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs324719	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs324722	0.80[ASN][1000 genomes]
rs324723	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324726	0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs324727	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324730	0.80[ASN][1000 genomes]
rs324731	0.80[ASN][1000 genomes]
rs324733	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324735	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs324740	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4262008	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4610362	0.92[JPT][hapmap]
rs60225400	0.83[ASN][1000 genomes]
rs60945555	0.83[ASN][1000 genomes]
rs6531816	0.84[GIH][hapmap];0.92[JPT][hapmap]
rs6531934	0.91[JPT][hapmap]
rs6827016	0.80[ASN][1000 genomes]
rs6834747	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856162	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs7657198	0.80[ASN][1000 genomes]
rs7663617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7684778	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7693127	0.80[ASN][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	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	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
4	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11732850	FAM47E	cis	parietal	SCAN
rs11732850	DLK2	trans	cerebellum	SCAN
rs11732850	USO1	cis	parietal	SCAN
rs11732850	CDKL2	cis	parietal	SCAN
rs11732850	SCARB2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
2	chr4:76599600-76621600	Weak transcription	Fetal Lung	lung
3	chr4:76599600-76623400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:76599600-76624000	Weak transcription	Brain Substantia Nigra	brain
5	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
7	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
9	chr4:76599800-76621200	Weak transcription	HepG2	liver
10	chr4:76599800-76627800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:76600600-76627000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:76605800-76623400	Weak transcription	K562	blood
14	chr4:76605800-76633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:76607400-76640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:76611400-76621200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:76612600-76622200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:76613000-76621600	Weak transcription	HSMMtube	muscle
19	chr4:76613000-76623400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:76613200-76627800	Weak transcription	A549	lung
21	chr4:76613400-76623400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:76613800-76621400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:76613800-76639000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:76613800-76639600	Weak transcription	Ovary	ovary
25	chr4:76614200-76621400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:76614600-76630200	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:76614800-76628200	Weak transcription	Gastric	stomach
28	chr4:76615600-76639800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:76615600-76639800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:76615800-76639000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:76616000-76640000	Weak transcription	Lung	lung
32	chr4:76616200-76630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:76617200-76621600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:76618200-76635000	Weak transcription	Adipose Nuclei	Adipose
35	chr4:76618400-76621200	Weak transcription	Stomach Mucosa	stomach
36	chr4:76618400-76639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:76618600-76623600	Weak transcription	Thymus	Thymus
38	chr4:76619000-76623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:76619400-76633400	Weak transcription	Fetal Kidney	kidney
40	chr4:76619600-76630400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:76620000-76621000	Enhancers	Right Ventricle	heart
42	chr4:76620000-76621400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr4:76620000-76621400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:76620000-76622000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr4:76620000-76622000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr4:76620000-76630400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:76620000-76640000	Weak transcription	Brain Germinal Matrix	brain
48	chr4:76620200-76621000	Enhancers	Psoas Muscle	Psoas
49	chr4:76620200-76621200	Enhancers	Primary T cells from cord blood	blood
50	chr4:76620200-76622200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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